![](\"../assets/img/octicon-package.png\")
GitHub: ![](\"../assets/img/github-alt.png\")
Maëlle Salmon and Scott Chamberlain introduced the new HTTP Testing in R book: Learn All About HTTP Testing: Book Update
Stefanie Butland and Steffi LaZerte wrote a post on Introducing the rOpenSci Community Contributing Guide
CRAN: GitHub:
v0.0.2) of tarchetypes is on CRAN - archetypes for targets. Checkout the docs to get started. v0.0.2) of targets is on CRAN - dynamic function-oriented make-like declarative workflows. Checkout the docs to get started. v0.13.5) of coder is on CRAN - deterministic categorization of items based on external code data. Checkout the docs to get started. v1.1.1) of webchem is on CRAN - Chemical information from the web. See the release notes for changes. Checkout the docs to get started. v0.6.0) of ckanr is on CRAN - client for the CKAN API. See the release notes for changes. Checkout the docs to get started. v7.13.1) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started. v1.0.0) of ritis is on CRAN - an R client for ITIS (Integrated Taxonomic Information Service). See the release notes for changes. Checkout the docs to get started. v0.3.2) of grainchanger is on CRAN - Data aggregation methods for raster data. See the release notes for changes. Checkout the docs to get started. v1.0.6) of essurvey is on CRAN - data from the European Social Survey. See the release notes for changes. Checkout the docs to get started. v1.2.0) of rebird is on CRAN - client for the eBird database of bird observations. See the release notes for changes. Checkout the vignette to get started. v3.5.2) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the docs to get started. v1.1.0) of gert is on CRAN - simple git client for R. See the release notes for changes. Checkout the docs to get started. v2.8) of assertr is on CRAN - Assertive Programming for R Analysis Pipelines. See the release notes for changes. Checkout the vignette to get started. v0.2.0) of rgnparser is on CRAN - parse scientific names using the Go tool gnparser. See the release notes for changes. Checkout the docs to get started. v3.0.0) of GSODR is on CRAN - Global Surface Summary of the Day (GSOD) Weather Data from R. See the release notes for changes. Checkout the docs to get started. v0.4.4) of nomisr is on CRAN - access UK official statistics from the Nomis database. See the release notes for changes. Checkout the docs to get started. v0.3.1) of git2rdata is on CRAN - store and retrieve data.frames in a Git repository. See the release notes for changes. Checkout the docs to get started. v0.7) of roadoi is on CRAN - find free versions of scholarly publications via Unpaywall. See the release notes for changes. Checkout the vignette to get started. v0.7.0) of rorcid is on CRAN - Interface to the Orcid.org API. See the release notes for changes. Checkout the vignette to get started. v1.4.0) of UCSCXenaTools is on CRAN - download and explore datasets from UCSC Xena data hubs. See the release notes for changes. Checkout the docs to get started. v3.1.5) of rfishbase is on CRAN - interface to Fishbase data. See the release notes for changes. Checkout the docs to get started. v0.3.0) of taxizedb is on CRAN - tools for working with taxonomic databases. See the release notes for changes. Checkout the docs to get started. v0.5.0) of weathercan is on CRAN - Download weather data from the Environment and Climate Change Canada website. See the release notes for changes. Checkout the docs to get started. v0.9.3) of hddtools is on CRAN - Hydrological Data Discovery Tools. See the release notes for changes. Checkout the docs to get started. v2.2.5) of ijtiff is on CRAN - comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started. v0.4.2) of nodbi is on CRAN - the NoSQL database connector. See the release notes for changes. Checkout the README to get started. v3.1.4) of qualtRics is on CRAN - download Qualtrics survey data. See the release notes for changes. Checkout the docs to get started. v0.9.4) of geojsonio is on CRAN - Convert Data from and to GeoJSON or TopoJSON. See the release notes for changes. Checkout the vignettes to get started. v2.6.0) of magick is on CRAN - Advanced graphics and Image-Processing in R. See the release notes for changes. Checkout the docs to get started. v1.4.1) of cld3 is on CRAN - Bindings to Google’s Compact Language Detector 3. See the release notes for changes. Checkout the docs to get started. We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following packages were recently approved:
The following packages were recently submitted:
Maëlle Salmon and Scott Chamberlain introduced the HTTP Testing in R book: Learn All About HTTP Testing: Book Update.
Stefanie Butland and Steffi LaZerte wrote a post on Introducing the rOpenSci Community Contributing Guide.
![](\"https://ropensci.org/blog/2021/01/20/contributing-guide/contrib_guide_cover_sm.png\")
Stefanie Butland and Emily Lescak wrote about How rOpenSci Runs Community Calls - arising from a presentation Stefanie gave to a Code for Science & Society Event.
![](\"https://ropensci.org/blog/2021/02/02/ropensci-community-calls/commcalls-img.png\")
Will Landau introduces his new packages targets - a new pipeline toolkit for R: targets: Democratizing Reproducible Analysis Pipelines. targets is the successor of drake, which succeeded remake.
![](\"../assets/img/targets.png\")
Lluís Revilla Sancho introduces the package BaseSet that recently went through rOpenSci Software Review: Introducing BaseSet for mathematical sets
Jeroen Ooms wrote about updates to the magick package: Behind the magick: updates to imagemagick and beyond
The following 15 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
Four new use cases were shared in the forum over the past month since our last newsletter:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Check out our guidance for taking over maintenance of a package.
We’ve had eight recent examples of maintainer transitions within rOpenSci:
We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.
Lucky, A., Atchison, R. A., Ohyama, L., Zhang, Y. M., Williams, J. L., Pinkney IV, J. L., … & Lippi, C. A. Myrmecology, Gender, and Geography: changing demographics of a research community over thirty years. Myrmecological News. https://bit.ly/3oVg7OU ↩
Bonnet, E., Jean-Pierre, D., & Paul, L. (2020). Optimizing Literature Search: TEMAS, A New Text-Mining Algorithm-Assisted Search Tool. https://www.researchsquare.com/article/rs-71504/latest.pdf ↩
Brightly, W. H., Hartley, S. E., Osborne, C. P., Simpson, K. J., & Strömberg, C. A. E. (2020). High silicon concentrations in grasses are linked to environmental conditions and not associated with C4 photosynthesis. Global Change Biology. https://doi.org/10.1111/gcb.15343 ↩
Germani, E., Lelouard, H., & Fallet, M. (2020). SAPHIR: a Shiny application to analyze tissue section images. F1000Research, 9, 1276. https://doi.org/10.12688/f1000research.27062.1 ↩
Fastovich, D., Russell, J. M., Jackson, S. T., Krause, T. R., Marcott, S. A., & Williams, J. W. (2020). Spatial Fingerprint of Younger Dryas Cooling and Warming in Eastern North America. Geophysical Research Letters. https://doi.org/10.1029/2020gl090031 ↩
Rycyk, A. M., Tyson Moore, R. B., Wells, R. S., McHugh, K. A., Berens McCabe, E. J., & Mann, D. A. (2020). Passive acoustic listening stations (PALS) show rapid onset of ecological effects of harmful algal blooms in real time. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-74647-z ↩
Wenndt, A., Sudini, H. K., Pingali, P., & Nelson, R. (2020). Exploring aflatoxin contamination and household-level exposure risk in diverse Indian food systems. PLOS ONE, 15(10), e0240565. https://doi.org/10.1371/journal.pone.0240565 ↩
Abbas, H. K., Zablotowicz, R. M., Bruns, H. A., & Abel, C. A. (2006). Biocontrol of aflatoxin in corn by inoculation with non-aflatoxigenicAspergillus flavusisolates. Biocontrol Science and Technology, 16(5), 437–449. https://doi.org/10.1080/09583150500532477 ↩
Jacobs, E., Bittig, H. C., Gräwe, U., Graves, C. A., Glockzin, M., Müller, J. D., … Rehder, G. (2020). Upwelling-induced trace gas dynamics in the Baltic Sea inferred from 8 years of autonomous measurements on a ship of opportunity. https://doi.org/10.5194/bg-2020-365 ↩
Hotez, P., Bottazzi, M. E., Strub-Wourgaft, N., Sosa-Estani, S., Torrico, F., Pajín, L., … Sancho, J. (2020). A new patient registry for Chagas disease. PLOS Neglected Tropical Diseases, 14(10), e0008418. https://doi.org/10.1371/journal.pntd.0008418 ↩
Raut, S. (2020). A computer vision approach to assess wood variability from whole-disk images of longleaf pine (Order No. 28023614). https://search.proquest.com/docview/2446699035 ↩
Cramer, M. T., Fidler, R. Y., Penrod, L. M., Carroll, J., & Turingan, R. G. (2020). A spatiotemporal comparison of length-at-age in the coral reef fish Acanthurus nigrofuscus between marine reserves and fished reefs. PLOS ONE, 15(9), e0239842. https://doi.org/10.1371/journal.pone.0239842 ↩
Winter-Billington, A., Moore, R. D., & Dadic, R. (2020). Evaluating the transferability of empirical models of debris-covered glacier melt. Journal of Glaciology, 1–18. https://doi.org/10.1017/jog.2020.57 ↩
Meng, B., Loonen, R. C. G. M., & Hensen, J. L. M. (2020). Data-driven inference of unknown tilt and azimuth of distributed PV systems. Solar Energy, 211, 418–432. https://doi.org/10.1016/j.solener.2020.09.077 ↩
Perez, T. M., & Feeley, K. J. (2020). Weak phylogenetic and climatic signals in plant heat tolerance. Journal of Biogeography. https://doi.org/10.1111/jbi.13984 ↩
Our own Maëlle Salmon was featured in an US-RSE Stories podcast. The US-RSE is The United States (US) Research Software Engineer Association. This is a great chance to learn more about Maëlle and some of the work she does.
Community Calls
Our next Community Call will cover Statistical Software Peer Review. The date is not yet set. See the link for more details.
Code of Conduct
Make sure to read our two recent posts on our Code of Conduct: rOpenSci Code of Conduct Annual Review and rOpenSci 2020 Code of Conduct Transparency Report
CRAN: GitHub:
v1.2.1) of cld2 is on CRAN - R wrapper for Google’s Compact Language Detector 2. See the release notes for changes. Checkout the docs to get started. v1.4.1) of cld3 is on CRAN - Bindings to Google’s Compact Language Detector 3. See the release notes for changes. Checkout the docs to get started. v0.28.0) of git2r is on CRAN - an interface to the libgit2 library, a pure C implementation of the Git core methods. See the release notes for changes. Checkout the docs to get started. v4.9.3) of plotly is on CRAN - Create Interactive Web Graphics via plotly.js. See the NEWS for changes. Checkout the plotly book to get started. v0.3.0) of PostcodesioR is on CRAN - API wrapper for Postcodes.io. See the release notes for changes. Checkout the docs to get started. v1.3.0) of rnoaa is on CRAN - NOAA Weather Data from R. See the release notes for changes. Checkout the docs to get started. v0.8.1) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. v0.7.2) of wellknown is on CRAN - Convert between WKT and GeoJSON. See the release notes for changes. Checkout the docs to get started. v1.0.3) of plater is on CRAN - read, tidy, and display data from microtiter plates. See the release notes for changes. Checkout the docs to get started. v3.4.2) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the docs to get started. v1.2.0) of spocc is on CRAN - an interface to many species occurrence data sources. See the release notes for changes. Checkout the docs to get started. v7.13.0) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started. v1.1-6) of suppdata is on CRAN - downloading supplementary data from published manuscripts. See the release notes for changes. Checkout the docs to get started. We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following package was recently submitted:
![](\"https://ropensci.org/blog/2020/12/22/phonfieldwork-phonetic-fieldwork-and-experiments/spec_example-1.png\")
The following 25 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
Two new use cases were shared in the forum over the past month since our last newsletter:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Check out our guidance for taking over maintenance of a package.
We’ve had eight recent examples of maintainer transitions within rOpenSci:
We’ve got three packages in need of a new maintainer. The current maintainer of all three packages is looking for new maintainers. Email Scott if you’re interested. If a new maintainer is not found these packages will be archived.
We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.
Grattarola, F., & Rodríguez-Tricot, L. (2020). Mammals of Paso Centurión, an area with relicts of Atlantic Forest in Uruguay. Neotropical Biology and Conservation, 15(3), 267–283. https://doi.org/10.3897/neotropical.15.e53062 ↩
Calderón Franco, D. (2020). Hi-C pipeline development for linking resistome and mobilome to the microbiome of wastewater samples https://bit.ly/3i7Q59d ↩
Hansen, E. R., & Jansa, J. M. (2020). Complexity, Resources, and Text Borrowing in State Legislatures. https://bit.ly/3nvLK0R ↩
Ilík, B. V. High-throughput sequencing as a tool for studying strongylid nematode communities in primates. Thesis. https://is.muni.cz/th/vg2vb/DP_Ilik_Vladislav.pdf ↩
Walton, S., Livermore, L., Bánki, O., Cubey, R., Drinkwater, R., Englund, M., … Wu, Z. (2020). Landscape Analysis for the Specimen Data Refinery. Research Ideas and Outcomes, 6. https://doi.org/10.3897/rio.6.e57602 ↩
Ossola, A., Hoeppner, M. J., Burley, H. M., Gallagher, R. V., Beaumont, L. J., & Leishman, M. R. (2020). The Global Urban Tree Inventory: A database of the diverse tree flora that inhabits the world’s cities. Global Ecology and Biogeography, 29(11), 1907–1914. https://doi.org/10.1111/geb.13169 ↩
Atwood, T. B., Valentine, S. A., Hammill, E., McCauley, D. J., Madin, E. M. P., Beard, K. H., & Pearse, W. D. (2020). Herbivores at the highest risk of extinction among mammals, birds, and reptiles. Science Advances, 6(32), eabb8458. https://doi.org/10.1126/sciadv.abb8458 ↩
Morgan, M., & Lovelace, R. (2020). Travel flow aggregation: Nationally scalable methods for interactive and online visualisation of transport behaviour at the road network level. Environment and Planning B: Urban Analytics and City Science, 239980832094277. https://doi.org/10.1177/2399808320942779 ↩
Carroll, L. M., Huisman, J. S., & Wiedmann, M. (2020). Twentieth-century emergence of antimicrobial resistant human- and bovine-associated Salmonella enterica serotype Typhimurium lineages in New York State. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-71344-9 ↩
Whitmer, S. L. M., Lo, M. K., Sazzad, H. M. S., Zufan, S., Gurley, E. S., Sultana, S., … Klena, J. D. (2020). Inference of Nipah virus Evolution, 1999-2015. Virus Evolution. https://doi.org/10.1093/ve/veaa062 ↩
Ettinger, C. L., & Eisen, J. A. (2020). Fungi, bacteria and oomycota opportunistically isolated from the seagrass, Zostera marina. PLOS ONE, 15(7), e0236135. https://doi.org/10.1371/journal.pone.0236135 ↩
Grassl, P., Schraffenberger, H., Zuiderveen Borgesius, F., & Buijzen, M. (2020, July 21). Dark and bright patterns in cookie consent requests. https://doi.org/10.31234/osf.io/gqs5h ↩
Scott, T. A., Ulibarri, N., & Perez Figueroa, O. (2020). NEPA and National Trends in Federal Infrastructure Siting in the United States. Review of Policy Research. https://doi.org/10.1111/ropr.12399 ↩
López Galán, A., Chung, W.-S., & Marshall, N. J. (2020). Dynamic Courtship Signals and Mate Preferences in Sepia plangon. Frontiers in Physiology, 11. https://doi.org/10.3389/fphys.2020.00845 ↩
Brandão, L. A. C., Agrelli, A., Bernardo, L., Paparella, F., Moura, R., & Crovella, S. (2020). PlatCOVID: A Novel Web Tool to Analyze, Curate and Share COVID-19 Literature. https://doi.org/10.21203/rs.3.rs-42169/v1 ↩
Wang, S., Xiong, Y., Gu, K., Zhao, L., Li, Y., Zhao, F., … Liu, X.-S. (2020). UCSCXenaShiny: An R Package for Exploring and Analyzing UCSC Xena Public Datasets in Web Browser. https://doi.org/10.20944/preprints202007.0179.v1 ↩
Obradovich, N., Özak, Ö., Martín, I., Ortuño-Ortín, I., Awad, E., Cebrián, M., … Cuevas, Á. (2020). Expanding the Measurement of Culture with a Sample of Two Billion Humans. National Bureau of Economic Research. https://doi.org/10.3386/w27827 ↩
Gutiérrez-Hernández, O. (2020). Fenología de los ecosistemas de alta montaña en Andalucía: Análisis de la tendencia estacional del SAVI (2000-2019). Pirineos, 175, 055. https://doi.org/10.3989/pirineos.2020.175005 ↩
Hazlett, M. A., Henderson, K. M., Zeitzer, I. F., & Drew, J. A. (2020). The geography of publishing in the Anthropocene. Conservation Science and Practice, 2(10). https://doi.org/10.1111/csp2.270 ↩
Mothes, C. C., Stemle, L. R., Fonseca, T. N., Clements, S. L., Howell, H. J., & Searcy, C. A. (2020). Protect or perish: Quantitative analysis of state‐level species protection supports preservation of the Endangered Species Act. Conservation Letters. https://doi.org/10.1111/conl.12761 ↩
Falconi, N., Fuller, T. K., DeStefano, S., & Organ, J. F. (2020). An open-access occurrence database for Andean bears in Peru. Ursus, 2020(31e11), 1. https://doi.org/10.2192/ursus-d-19-00012.1 ↩
Costanzi, S., Slavick, C. K., Hutcheson, B. O., Koblentz, G. D., & Cupitt, R. T. (2020). Lists of Chemical Warfare Agents and Precursors from International Nonproliferation Frameworks: Structural Annotation and Chemical Fingerprint Analysis. Journal of Chemical Information and Modeling, 60(10), 4804–4816. https://doi.org/10.1021/acs.jcim.0c00896 ↩
Batista, E., Lopes, A., & Alves, A. (2020). Botryosphaeriaceae species on forest trees in Portugal: diversity, distribution and pathogenicity. European Journal of Plant Pathology, 158(3), 693–720. https://doi.org/10.1007/s10658-020-02112-8 ↩
Rasher, D. B., Steneck, R. S., Halfar, J., Kroeker, K. J., Ries, J. B., Tinker, M. T., … Estes, J. A. (2020). Keystone predators govern the pathway and pace of climate impacts in a subarctic marine ecosystem. Science, 369(6509), 1351–1354. https://doi.org/10.1126/science.aav7515 ↩
Kuchta, R., Řehulková, E., Francová, K., Scholz, T., Morand, S., & Šimková, A. (2020). Diversity of monogeneans and tapeworms in cypriniform fishes across two continents. International Journal for Parasitology, 50(10-11), 771–786. https://doi.org/10.1016/j.ijpara.2020.06.005 ↩
Community Calls
Join us for our next Community Call - The Wild World of Data Repositories - this Wednesday, December 16th, 2020 (10-11 AM PST). This call will be moderated by Kara Woo with speakers Daniella Lowenberg, Matt Jones, Carl Boettiger and Karthik Ram.
CRAN: GitHub:
v0.1.1) of outsider is on CRAN - “Install and Run Programs, Outside of R, Inside of R”. Checkout the docs to get started. v0.0.2) of allcontributors is on CRAN - Acknowledge all Contributors to a Project. Checkout the docs to get started. v0.6.0) of vcr is on CRAN - record HTTP calls to disk for test caching. See the release notes for changes. Checkout the HTTP testing book to get started. v0.0.4) of medrxivr is on CRAN - access and search MedRxiv and BioRxiv preprint data. See the release notes for changes. Checkout the docs to get started. v3.0.1) of hunspell is on CRAN - High-Performance stemmer, tokenizer, and spell checker. See the release notes for changes. Checkout the vignette to get started. v0.3.1) of tacmagic is on CRAN - positron emission tomography time-activity curve analysis. See the release notes for changes. Checkout the vignette to get started. v0.7.4) of webmockr is on CRAN - stubbing and setting expectations on HTTP requests. See the release notes for changes. Checkout the HTTP testing book to get started. v1.13) of mcbette is on CRAN - model comparison using babette. See the release notes for changes. Checkout the docs to get started. v0.2.0) of prism is on CRAN - Data from the Oregon State Prism Climate Project. See the release notes for changes. Checkout the vignette to get started. v3.4.0) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the occurrence manual to get started. v0.3.0) of jaod is on CRAN - Directory of Open Access Journals client. See the release notes for changes. Checkout the docs to get started. v1.1.1) of rnpn is on CRAN - Interface to the National Phenology Network API. See the release notes for changes. Checkout the docs to get started. v0.7.3) of bomrang is on CRAN - Australian government Bureau of Meteorology (BOM) data. See the release notes for changes. Checkout the docs to get started. v0.7.1) of rdhs is on CRAN - Client for Demographic and Health Survey (DHS) Data. See the release notes for changes. Checkout the docs to get started. v0.4.3) of auk is on CRAN - eBird data extraction and processing. See the release notes for changes. Checkout the docs to get started. v0.0.10) of phonfieldwork is on CRAN - linguistic phonetic fieldwork tools. See the release notes for changes. Checkout the docs to get started. v1.3.6) of UCSCXenaTools is on CRAN - download and explore datasets from UCSC Xena data hubs. See the release notes for changes. Checkout the docs to get started. We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following packages were recently submitted:
Richèl Bilderbeek wrote about using his mcbette package for: Selecting the Best Phylogenetic Evolutionary Model
![](\"https://ropensci.org/blog/2020/12/01/mcbette-selecting-the-best-inference-model/plot_densitree-1.png\")
Dennis Irorere wrote a post about solving a problem using a GraphQL service using the rOpenSci package ghql: Accessing GrahpQL from R
![](\"https://ropensci.org/blog/2020/12/08/accessing-grahpql-in-r/GHQL.png\")
The following 22 works use/cite rOpenSci software:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Check out our guidance for taking over maintenance of a package.
We’ve had eight recent examples of maintainer transitions within rOpenSci:
We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.
Reimuth, J., & Zotz, G. (2020). The biogeography of the megadiverse genus Anthurium (Araceae). Botanical Journal of the Linnean Society, 194(2), 164-176. https://doi.org/10.1093/botlinnean/boaa044 ↩
Yu, V., Wyatt, S., Woodall, M., Sultan, M., Klaire, V., Bailey, K., & Mohammed, M. A. (2020). Impact of Vertical Integration of General Practices with an Acute Hospital on Hospital Admissions: a Retrospective Synthetic Matched Controlled Database Study. https://bit.ly/3gN1omx ↩
Koch, L. K., Cunze, S., Kochmann, J., & Klimpel, S. (2020). Bats as putative Zaire ebolavirus reservoir hosts and their habitat suitability in Africa. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-71226-0 ↩
Göbel, S. (2020). Voting and Social Media-Based Political Participation. SocArXiv https://doi.org/10.31235/osf.io/sjq4g ↩
Larouche, O., Benton, B., Corn, K. A., Friedman, S. T., Gross, D., Iwan, M., … Price, S. A. (2020). Reef-associated fishes have more maneuverable body shapes at a macroevolutionary scale. Coral Reefs, 39(5), 1427–1439. https://doi.org/10.1007/s00338-020-01976-w ↩
De Sousa, K., & Solberg, S. Ø. (2020). Conservation Gaps in Traditional Vegetables Native to Europe and Fennoscandia. Agriculture, 10(8), 340. https://doi.org/10.3390/agriculture10080340 ↩
Polaina, E., Pärt, T., & Recio, M. R. (2020). Identifying hotspots of invasive alien terrestrial vertebrates in Europe to assist transboundary prevention and control. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-68387-3 ↩
Ihaka, R., & Gentleman, R. (1996). R: A Language for Data Analysis and Graphics. Journal of Computational and Graphical Statistics, 5(3), 299–314. https://doi.org/10.1080/10618600.1996.10474713 ↩
Mothes, C. C., Howell, H. J., & Searcy, C. A. (2020). Habitat suitability models for the imperiled wood turtle (Glyptemys insculpta) raise concerns for the species’ persistence under future climate change. Global Ecology and Conservation, 24, e01247. https://doi.org/10.1016/j.gecco.2020.e01247 ↩
Scott, A. 2020. Spatial variation in PM2. 5 concentrations across Timaru. Report, Environment Canterbury Regional Council https://bit.ly/3icvorg ↩
Tonnis, B., Wang, M. L., Li, X., Wang, J., Puppala, N., Tallury, S., & Yu, J. (2020). Peanut FAD2 Genotype and Growing Location Interactions Significantly Affect the Level of Oleic Acid in Seeds. Journal of the American Oil Chemists’ Society, 97(9), 1001–1010. https://doi.org/10.1002/aocs.12401 ↩
Da Silva Abel, E. L., Delgado, R. C., Vilanova, R. S., Teodoro, P. E., da Silva Junior, C. A., Abreu, M. C., & Silva, G. F. C. (2020). Environmental dynamics of the Juruá watershed in the Amazon. Environment, Development and Sustainability. https://doi.org/10.1007/s10668-020-00890-z ↩
Vantas, K., Sidiropoulos, E., & Evangelides, C. (2020). Estimating Rainfall Erosivity from Daily Precipitation Using Generalized Additive Models. Environmental Sciences Proceedings, 2(1), 21. https://doi.org/10.3390/environsciproc2020002021 ↩
Weber, A. (2020). Digital elevation models of German waterway and navigation. Report. http://doi.bafg.de/BfG/2020/BfG-2011.pdf ↩
Nania, D., Flecks, M., & Rödder, D. (2020). Continuous expansion of the geographic range linked to realized niche expansion in the invasive Mourning gecko Lepidodactylus lugubris (Duméril & Bibron, 1836). PLOS ONE, 15(7), e0235060. https://doi.org/10.1371/journal.pone.0235060 ↩
Keppeler, F. W., Montaña, C. G., & Winemiller, K. O. (2020). The relationship between trophic level and body size in fishes depends on functional traits. Ecological Monographs. https://doi.org/10.1002/ecm.1415 ↩
Doyle, M. A., Schurer, S., & Silburn, S. (2020). Unintended Consequences of Welfare Reform: Evidence from Birth Outcomes of Aboriginal Australians. SSRN. http://ftp.iza.org/dp13543.pdf ↩
Sass, C. A. B., Pimentel, T. C., Aleixo, M. G. B., Dantas, T. M., Cyrino Oliveira, F. L., Freitas, M. Q., … Esmerino, E. A. (2020). Exploring social media data to understand consumers’ perception of eggs: A multilingual study using Twitter. Journal of Sensory Studies. https://doi.org/10.1111/joss.12607 ↩
Allerton, T. A. P. (2020). Functional Attributes of Post-Disturbance Regeneration in Puerto Rican Tropical Dry Forest. Dissertation Thesis. https://bit.ly/2R9upwT ↩
Davies, A. D., Lewis, Z., & Dougherty, L. R. (2020). A meta-analysis of factors influencing the strength of mate-choice copying in animals. Behavioral Ecology. https://doi.org/10.1093/beheco/araa064 ↩
Becker, D. J., & Han, B. A. (2020). The macroecology and evolution of avian competence for Borrelia burgdorferi. bioRxiv https://doi.org/10.1101/2020.04.15.040352 ↩
Greenville, A. C., Newsome, T. M., Wardle, G. M., Dickman, C. R., Ripple, W. J., & Murray, B. R. (2020). Simultaneously operating threats cannot predict extinction risk. Conservation Letters. https://doi.org/10.1111/conl.12758 ↩
Community Calls
Join us for our next Community Call - The Wild World of Data Repositories - on Wednesday, December 16th, 2020 (10-11 AM PST). This call will be moderated by Kara Woo with speakers Daniella Lowenberg, Matt Jones, Carl Boettiger and Karthik Ram.
Software Review
We’re thrilled to announce three new rOpenSci Software Review Editors: Laura DeCicco, Julia Gustavsen, Mauro Lepore
CRAN: GitHub:
v1.12) of mcbette is on CRAN - model comparison using babette. Checkout the docs to get started. This package recently went through rOpenSci software review. v0.0.14) of BaseSet is on CRAN - working with sets the tidy way. Checkout the docs to get started. This package recently went through rOpenSci software review. v0.1.0) of rgnparser is on CRAN - parse scientific names using the Go tool gnparser. Checkout the docs to get started. v1.0.0) of dataspice is on CRAN - create lightweight Schema.org descriptions of data. Checkout the docs to get started. v0.2.0) of taxlist is on CRAN - handling taxonomic lists. Checkout the docs to get started. This package recently went through rOpenSci software review. v0.4.3) of auk is on CRAN - eBird data extraction and processing. See the release notes for changes. Checkout the docs to get started. v1.3.6) of UCSCXenaTools is on CRAN - download and explore datasets from UCSC Xena data hubs. See the release notes for changes. Checkout the docs to get started. v0.6.0) of microdemic is on CRAN - Microsoft Academic API client. See the release notes for changes. Checkout the README to get started. v0.7.2) of bomrang is on CRAN - Australian government Bureau of Meteorology (BOM) data. See the release notes for changes. Checkout the docs to get started. v0.4.2) of nlrx is on CRAN - setup, run and analyze NetLogo model simulations. See the release notes for changes. Checkout the docs to get started. v0.5.2) of tidyhydat is on CRAN - Water Survey of Canada hydrometric data. See the release notes for changes. Checkout the docs to get started. v1.2.0) of jqr is on CRAN - a client for JQ, the JSON processor. See the release notes for changes. Checkout the docs to get started. v1.3.0) of RefManageR is on CRAN - tools for importing and working with bibliographic references. See the NEWS for changes. Checkout the vignettes to get started. v1.0.2) of gert is on CRAN - simple git client for R. See the release notes for changes. Checkout the docs to get started. v2.0.4) of EML is on CRAN - read and write ecological metadata language files. See the release notes for changes. Checkout the docs to get started. v2.5.2) of magick is on CRAN - Advanced graphics and Image-Processing in R. See the release notes for changes. Checkout the docs to get started. v1.2.3) of rentrez is on CRAN - ENTREZ in R. See the release notes for changes. Checkout the docs to get started. v0.2.11) of ropenaq is on CRAN - air quality data from the open data platform OpenAQ. See the release notes for changes. Checkout the docs to get started. v2.2.4) of ijtiff is on CRAN - comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started. v0.3.1) of opentripplanner is on CRAN - client for OpenTripPlanner for journey planning. See the release notes for changes. Checkout the docs to get started. v2.2) of babette is on CRAN - control BEAST2 from R. See the release notes for changes. Checkout the docs to get started. v0.0.8) of arkdb is on CRAN - archive and unarchive databases as flat text files. See the release notes for changes. Checkout the docs to get started. v1.4.0) of datapack is on CRAN - flexible container to transport and manipulate data. See the release notes for changes. Checkout the docs to get started. v0.1.4) of gitignore is on CRAN - create useful .gitignore files for your project. See the release notes for changes. Checkout the docs to get started. v0.1.4) of osmdata is on CRAN - import OpenStreetMap data as simple features or spatial objects. See the release notes for changes. Checkout the docs to get started. v0.7.0) of rerddap is on CRAN - General Purpose Client for ERDDAP Servers. See the release notes for changes. Checkout the docs to get started. v2.3) of mauricer is on CRAN - install BEAST2 packages. See the release notes for changes. Checkout the docs to get started. v1.1-5) of suppdata is on CRAN - downloading supplementary data from published manuscripts. See the release notes for changes. Checkout the vignette to get started. v2.2.1) of beastier is on CRAN - Provides a way to call BEAST2 from R. See the release notes for changes. Checkout the docs to get started. v0.9.99) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started. v0.7.0) of rredlist is on CRAN - IUCN Red List client. See the release notes for changes. Checkout the README to get started. v0.0.9) of plotdap is on CRAN - easily visualize data from ERDDAP servers via the rerddap package. See the release notes for changes. Checkout the vignette to get started. v0.8.0) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. v7.12.7) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started. v0.3.2) of getCRUCLdata is on CRAN - use and explore CRU CL v. 2.0 climatology elements. See the release notes for changes. Checkout the docs to get started. We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following package was recently approved:
The following packages were recently submitted:
Liam Brierley wrote a very nice post on our blog about using some rOpenSci tools to study Coronaviruses: Using Open-Access Tools (rentrez, taxize) to Find Coronaviruses, Their Genetic Sequences, and Their Hosts
![](\"https://ropensci.org/blog/2020/11/10/coronaviruses-and-hosts/pipeline.png\")
Scott Chamberlain wrote a post titled fulltext: Behind the Scenes, going behind the scenes of the fulltext package. The post describes the wandering path the package has gone through to help R users obtain full text versions of scholarly articles for text-mining, including working with Crossref, to building custom web APIs and balancing performance against other considerations.
Jeroen Ooms wrote a post about the V8 package: Installing V8 is now even easier.
![](\"https://v8.dev/_img/v8.svg\")
Jeroen Ooms wrote a post on: Moving away from Travis CI.
![](\"https://ropensci.org/assets/blog-images/travis.png\")
The following 20 works use/cite rOpenSci software:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Check out our guidance for taking over maintenance of a package.
We’ve had eight recent examples of maintainer transitions within rOpenSci:
We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.
Bayley, D. T. I., Purvis, A., Nellas, A. C., Arias, M., & Koldewey, H. J. (2020). Measuring the long-term success of small-scale marine protected areas in a Philippine reef fishery. Coral Reefs. https://doi.org/10.1007/s00338-020-01987-7 ↩
Carraro, L., Mächler, E., Wüthrich, R., & Altermatt, F. (2020). Environmental DNA allows upscaling spatial patterns of biodiversity in freshwater ecosystems. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-17337-8 ↩
Weyna, A., & Romiguier, J. (2020). Relaxation of purifying selection suggests low effective population size in eusocial Hymenoptera and solitary pollinating bees. https://doi.org/10.1101/2020.04.14.038893 ↩
Sanchez‐Martinez, P., Martínez‐Vilalta, J., Dexter, K. G., Segovia, R. A., & Mencuccini, M. (2020). Adaptation and coordinated evolution of plant hydraulic traits. Ecology Letters. https://doi.org/10.1111/ele.13584 ↩
Feenstra, B. (2020). Development of Methodologies for the Use and Application of Air Quality Sensors to Enable Community Air Monitoring (Doctoral dissertation, UC Riverside) https://escholarship.org/content/qt0659j8sn/qt0659j8sn.pdf ↩
Westgate, M. J., Barton, P. S., Lindenmayer, D. B., & Andrew, N. R. (2020). Quantifying shifts in topic popularity over 44 years of Austral Ecology. Austral Ecology, 45(6), 663–671. https://doi.org/10.1111/aec.12938 ↩
Behrendt, I., Fasshauer, M., & Eichner, G. (2020). Gluten intake and metabolic health: conflicting findings from the UK Biobank. European Journal of Nutrition. https://doi.org/10.1007/s00394-020-02351-9 ↩
Chugunkova, A. V., & Pyzhev, A. I. (2020). Impacts of Global Climate Change on Duration of Logging Season in Siberian Boreal Forests. Forests, 11(7), 756. https://doi.org/10.3390/f11070756 ↩
Kakioka, R., Mori, S., Kokita, T., Hosoki, T. K., Nagano, A. J., Ishikawa, A., … Kitano, J. (2020). Multiple waves of freshwater colonization of the three-spined stickleback in the Japanese Archipelago. https://doi.org/10.21203/rs.3.rs-59443/v1 ↩
Hovorka, A. (2020). Predictive Modeling in Fugitive Emissions Testing. Thesis. https://shareok.org/bitstream/handle/11244/325365/2020_Hovorka_Abigail_Faye_Thesis.pdf?sequence=2 ↩
Montero-Manso, P., & Hyndman, R. J. (2020). Principles and Algorithms for Forecasting Groups of Time Series: Locality and Globality. arXiv preprint arXiv:2008.00444 https://arxiv.org/pdf/2008.00444.pdf ↩
Feenstra, B., Collier-Oxandale, A., Papapostolou, V., Cocker, D., & Polidori, A. (2020). The AirSensor open-source R-package and DataViewer web application for interpreting community data collected by low-cost sensor networks. Environmental Modelling & Software, 134, 104832. https://doi.org/10.1016/j.envsoft.2020.104832 ↩
Li, M. Application of automatic sentiment analysis: The role of emotions in an experimental learning intervention. https://psyarxiv.com/upfs9/download?format=pdf ↩
Kuempel, C. D., Frazier, M., Nash, K. L., Jacobsen, N. S., Williams, D. R., Blanchard, J. L., … Halpern, B. S. (2020). Integrating Life Cycle and Impact Assessments to Map Food’s Cumulative Environmental Footprint. One Earth, 3(1), 65–78. https://doi.org/10.1016/j.oneear.2020.06.014 ↩
Laguna, L., Fiszman, S., Puerta, P., Chaya, C., & Tárrega, A. (2020). The impact of COVID-19 lockdown on food priorities. Results from a preliminary study using social media and an online survey with Spanish consumers. Food Quality and Preference, 86, 104028. https://doi.org/10.1016/j.foodqual.2020.104028 ↩
Sodhi, K., Wang, X., Chaudhry, M. A., Lakhani, H. V., Zehra, M., Pratt, R., … Shapiro, J. I. (2020). Central Role for Adipocyte Na,K-ATPase Oxidant Amplification Loop in the Pathogenesis of Experimental Uremic Cardiomyopathy. Journal of the American Society of Nephrology, 31(8), 1746–1760. https://doi.org/10.1681/asn.2019101070 ↩
Minoli I., Pérez C.H.F., Morando M., Avila L.J. (2020) Biogeography, Ecology, and Spatial Patterns of Patagonian Lizards. In: Morando M., Avila L. (eds) Lizards of Patagonia. Natural and Social Sciences of Patagonia. Springer, Cham. https://doi.org/10.1007/978-3-030-42752-8_8 ↩
Yeşilkanat, C. M. (2020). Spatio-temporal estimation of the daily cases of COVID-19 in worldwide using random forest machine learning algorithm. Chaos, Solitons & Fractals, 140, 110210. https://doi.org/10.1016/j.chaos.2020.110210 ↩
Kopp, T., & Salecker, J. (2020). How traders influence their neighbours: Modelling social evolutionary processes and peer effects in agricultural trade networks. Journal of Economic Dynamics and Control, 117, 103944. https://doi.org/10.1016/j.jedc.2020.103944 ↩
Aragão e Pina, J., Passos, A. M., Maynard, M. T., & Sinval, J. (2021). Self-efficacy, mental models and team adaptation: A first approach on football and futsal refereeing. Psychology of Sport and Exercise, 52, 101787. https://doi.org/10.1016/j.psychsport.2020.101787 ↩
We’ve just released the fifth version (v0.5) of the rOpenSci Developer Guide. Some noteable updates:
On Oct 22, our Community Manager Stefanie Butland, and Software Peer Review Editor Brooke Anderson, presented to R-Ladies East Lansing and Chicago about our Community Contributing Guide and software peer review process. Brooke’s slides
CRAN: GitHub:
v0.3.2) of getCRUCLdata is on CRAN - use and explore CRU CL v. 2.0 climatology elements. See the release notes for changes. Checkout the docs to get started. v0.0.9) of phonfieldwork is on CRAN - linguistic phonetic fieldwork tools. See the release notes for changes. Checkout the docs to get started. v3.0.1) of nasapower is on CRAN - NASA POWER API Client. See the release notes for changes. Checkout the docs to get started. v0.3.0) of opentripplanner is on CRAN - client for OpenTripPlanner for journey planning. See the release notes for changes. Checkout the docs to get started. v0.0.8) of plotdap is on CRAN - easily visualize data from ERDDAP servers via the rerddap package. See the release notes for changes. Checkout the vignette to get started. v3.0.11) of rotl is on CRAN - an interface to the Open Tree of Life API. See the release notes for changes. Checkout the vignettes to get started. v0.1.15) of spatsoc is on CRAN - detecting spatial and temporal groups in GPS relocations. See the release notes for changes. Checkout the docs to get started. v0.7.0) of wellknown is on CRAN - Convert between WKT and GeoJSON. See the release notes for changes. Checkout the vignette to get started. v0.4.2) of auk is on CRAN - eBird data extraction and processing. See the release notes for changes. Checkout the docs to get started. v1.6.0) of fulltext is on CRAN - full text of scholarly articles across many data sources. See the release notes for changes. Checkout the fulltext book to get started. v2.2.2) of ijtiff is on CRAN - comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started. v2.2) of spelling is on CRAN - tools for spell checking. See the release notes for changes. Checkout the README to get started. v2.2) of beastier is on CRAN - Provides a way to call BEAST2 from R. See the release notes for changes. Checkout the docs to get started. v2.4) of beautier is on CRAN - create BEAST2 input files programmatically. See the release notes for changes. Checkout the docs to get started. v2.5.0) of magick is on CRAN - Advanced graphics and Image-Processing in R. See the release notes for changes. Checkout the vignette to get started. v0.0.7) of arkdb is on CRAN - archive and unarchive databases as flat text files. See the release notes for changes. Checkout the docs to get started. v0.3.0) of handlr is on CRAN - Convert among citation formats. See the release notes for changes. Checkout the docs to get started. v1.0.1) of gert is on CRAN - simple git client for R. See the release notes for changes. Checkout the docs to get started. v2.0-18) of CoordinateCleaner is on CRAN - automated cleaning of occurrence records from biological collections. See the release notes for changes. Checkout the docs to get started. v0.5.1) of iheatmapr is on CRAN - Interactive and complex heatmaps. See the release notes for changes. Checkout the docs to get started. v0.1.6) of rinat is on CRAN - R client for iNaturalist APIs. See the release notes for changes. Checkout the docs to get started. v2.0.4) of MODIStsp is on CRAN - Automate Download and Preprocessing of MODIS Land Products Data. See the release notes for changes. Checkout the docs to get started. v0.3.0) of parzer is on CRAN - parse messy geographic coordinates. See the release notes for changes. Checkout the docs to get started. v0.2.2) of rbace is on CRAN - Bielefeld Academic Search Engine (BASE) client. See the release notes for changes. Checkout the docs to get started. v2.0.2) of rmangal is on CRAN - interface to the Mangal database of ecological networks. See the release notes for changes. Checkout the docs to get started. v0.5.2) of mapr is on CRAN - visualize species occurrence data. See the release notes for changes. Checkout the vignette to get started. We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following package was recently approved:
The following package was recently submitted:
It’s time for another installment of … 2 Months in 2 Minutes - rOpenSci News, October 2020 - if you want a brief summary of the last 2 months of these newsletters, these blog posts are for you (written by Stefanie Butland)
Zhang-He Goh, Jonny Coates, and Hugo Gruson wrote a blog post that was cross-posted on the preLights blog: Covidpreprints.com: Automating Website Updates with the europepmc and rAltmetric Packages. In the post, they detail how they have used rOpenSci packages rAltmetric and europepmc (in addition to other R packages) to automate updating covidpreprints.com.
Software Review
Luke McGuinness wrote about his recently rOpenSci reviewed package medrxivr: Searching medRxiv and bioRxiv Preprint Data. He discusses the motivation behind the package, and highlights cases for medrxivr.
The following 21 works use/cite rOpenSci software:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Check out our guidance for taking over maintenance of a package.
We’ve had eight recent examples of maintainer transitions within rOpenSci:
We’ve got one package in need of a new maintainer:
We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.
Bauder, J. M., Stodola, K. W., Benson, T. J., Miller, C. A., & Allen, M. L. (2020). Raccoon Pelt Price and Trapper Harvest Relationships Are Temporally Inconsistent. The Journal of Wildlife Management. https://doi.org/10.1002/jwmg.21928 ↩
Nalley, E. (2020). Picky eater or generalist feeder? Diet diversity and functional homogenization in herbivorous reef fishes (Doctoral dissertation, University of Hawai’i at Manoa). https://bit.ly/34wYk9y ↩
Kleinschroth, F., Winton, R. S., Calamita, E., Niggemann, F., Botter, M., Wehrli, B., & Ghazoul, J. (2020). Living with floating vegetation invasions. Ambio. https://doi.org/10.1007/s13280-020-01360-6 ↩
Göbel, S. 2020. Voting and Social Media-Based Political Participation. https://doi.org/10.31235/osf.io/sjq4g ↩
Calero Valdez A. (2020) Making Reproducible Research Simple Using RMarkdown and the OSF. In: Meiselwitz G. (eds) Social Computing and Social Media. Design, Ethics, User Behavior, and Social Network Analysis. HCII 2020. Lecture Notes in Computer Science, vol 12194. Springer, Cham. https://link.springer.com/chapter/10.1007/978-3-030-49570-1_3 ↩
Roa-Ureta, R. H., Henríquez, J., & Molinet, C. (2020). Achieving sustainable exploitation through co-management in three Chilean small-scale fisheries. Fisheries Research, 230, 105674. https://doi.org/10.1016/j.fishres.2020.105674 ↩
Ramiller, A. J. (2020). Don’t Destroy Our Neighborhood: Neighborhood Imaginaries and the Politics of Upzoning/Displacement through Development: Spatial and Temporal Dynamics of Residential Eviction and Capital Investment (Doctoral dissertation). https://bit.ly/2TtRE5P ↩
Lawlor, J. A., & Arellano, S. M. (2020). Temperature and salinity, not acidification, predict near-future larval growth and larval habitat suitability of Olympia oysters in the Salish Sea. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-69568-w ↩
Puschmann, C., & Pentzold, C. (2020). A field comes of age: tracking research on the internet within communication studies, 1994 to 2018. Internet Histories, 1–19. https://doi.org/10.1080/24701475.2020.1749805 ↩
Cahill, C. L., Anderson, S. C., Paul, A. J., MacPherson, L., Sullivan, M. G., van Poorten, B. T., … & Post, J. R. (2020). A spatial-temporal approach to modeling somatic growth across inland recreational fisheries landscapes. Canadian Journal of Fisheries and Aquatic Sciences, (ja). https://cdnsciencepub.com/doi/abs/10.1139/cjfas-2019-0434 ↩
Colli‐Silva, M., Reginato, M., Cabral, A., Forzza, R. C., Pirani, J. R., & Vasconcelos, T. N. da C. (2020). Evaluating shortfalls and spatial accuracy of biodiversity documentation in the Atlantic Forest, the most diverse and threatened Brazilian phytogeographic domain. TAXON, 69(3), 567–577. https://doi.org/10.1002/tax.12239 ↩
Madritsch, S., Bomers, S., Posekany, A., Burg, A., Birke, R., Emerstorfer, F., … Sehr, E. M. (2020). Integrative transcriptomics reveals genotypic impact on sugar beet storability. Plant Molecular Biology. https://doi.org/10.1007/s11103-020-01041-8 ↩
Kamiński, M., Muth, A., & Bogdański, P. (2020). Smoking, Vaping, and Tobacco Industry During COVID-19 Pandemic: Twitter Data Analysis. Cyberpsychology, Behavior, and Social Networking. https://doi.org/10.1089/cyber.2020.0384 ↩
Torregroza Espinosa, A. C. (2020). Spatio-temporal distribution of temperature, salinity and suspended sediment on the deltaic front of the Magdalena River: Influence on nutrient concentration and primary productivity. PhD Thesis. https://bit.ly/3jCPUCc ↩
Mancosu, M., & Vegetti, F. (2020). What You Can Scrape and What Is Right to Scrape: A Proposal for a Tool to Collect Public Facebook Data. Social Media + Society, 6(3), 205630512094070. https://doi.org/10.1177/2056305120940703 ↩
Li, Z. R., Martin, B. D., Dong, T. Q., Fuglstad, G. A., Paige, J., Riebler, A., … & Wakefield, J. (2020). Space-Time Smoothing of Demographic and Health Indicators using the R Package SUMMER. arXiv preprint arXiv:2007.05117 https://arxiv.org/pdf/2007.05117. ↩
Foster, Z. S. L. (2020). Development of Computational, Visualization, and Molecular Tools for Fungal and Oomycete Community Ecology. PhD Dissertation. Oregon State University. https://ir.library.oregonstate.edu/downloads/qr46r6685 ↩
Portik, D. M., & Wiens, J. J. (2020). Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses? Systematic Biology. https://doi.org/10.1093/sysbio/syaa064 ↩
Brandão, L. A. C., Agrelli, A., Bernardo, L., Paparella, F., Moura, R., & Crovella, S. (2020). PlatCOVID: A Novel Web Tool to Analyze, Curate and Share COVID-19 Literature. https://doi.org/10.21203/rs.3.rs-42169/v1 ↩
Larouche, O., Hodge, J. R., Alencar, L. R. V., Camper, B., Adams, D. S., Zapfe, K., … Price, S. A. (2020). Do key innovations unlock diversification? A case-study on the morphological and ecological impact of pharyngognathy in acanthomorph fishes. Current Zoology. https://doi.org/10.1093/cz/zoaa048 ↩
Lakoba, V. T., Brooks, R. K., Haak, D. C., & Barney, J. N. (2020). An Analysis of US State Regulated Weed Lists: A Discordance between Biology and Policy. BioScience, 70(9), 804–813. https://doi.org/10.1093/biosci/biaa081 ↩
CRAN: GitHub:
v0.1.0) of treedata.table is on CRAN - manipulation of matched phylogenies and data using data.table. Checkout the docs to get started. v0.1.3) of dittodb is on CRAN - a test environment for database requests. See the release notes for changes. Checkout the docs to get started. v7.12.6) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started. v2.2.1) of ijtiff is on CRAN - comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started. v3.0.0) of nasapower is on CRAN - NASA POWER API Client. See the release notes for changes. Checkout the docs to get started. v0.5.1) of tidyhydat is on CRAN - Water Survey of Canada hydrometric data. See the release notes for changes. Checkout the vignettes to get started. v0.2.0) of parzer is on CRAN - parse messy geographic coordinates. See the release notes for changes. Checkout the docs to get started. v0.3.0) of pleiades is on CRAN - interface to the Pleiades archeological database. See the release notes for changes. Checkout the docs to get started. v1.4.0) of skynet is on CRAN - Bureau of Transport Statistics Data client. See the release notes for changes. Checkout the docs to get started. v0.2.0) of taxlist is on CRAN - handling taxonomic lists. See the release notes for changes. Checkout the docs to get started. v1.2.0) of rnoaa is on CRAN - NOAA Weather Data from R. See the release notes for changes. Checkout the docs to get started. v1.1-4) of suppdata is on CRAN - downloading supplementary data from published manuscripts. See the release notes for changes. Checkout the vignette to get started. v1.1.4) of lingtypology is on CRAN - linguistic typology and mapping. See the release notes for changes. Checkout the docs to get started. v0.1.2) of binman is on CRAN - a binary download manager. See the release notes for changes. Checkout the vignette to get started. v1.1.0) of rcrossref is on CRAN - R client for the Crossref API. See the release notes for changes. Checkout the docs to get started. v1.1.0) of webchem is on CRAN - Chemical information from the web. See the release notes for changes. Checkout the docs to get started. v1.3.0) of stats19 is on CRAN - Work with Open Road Traffic Casualty Data from Great Britain. See the release notes for changes. Checkout the docs to get started. v1.3.4) of UCSCXenaTools is on CRAN - download and explore datasets from UCSC Xena data hubs. See the release notes for changes. Checkout the docs to get started. v0.7.0) of webmockr is on CRAN - stubbing and setting expectations on HTTP requests. See the release notes for changes. Checkout the HTTP testing book to get started. v0.5.1) of av is on CRAN - working with audio and video. See the release notes for changes. Checkout the docs to get started. v0.7.1) of bomrang is on CRAN - Australian government Bureau of Meteorology (BOM) data. See the release notes for changes. Checkout the docs to get started. v0.0.3) of medrxivr is on CRAN - access and search MedRxiv and BioRxiv preprint data. See the release notes for changes. Checkout the docs to get started. We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following package was recently approved:
The following package was recently submitted:
Our community manager Stefanie Butland wrote the post Hacktober? Any Month is a Good Month to Contribute to rOpenSci - with guidance on how to make your package easier to contribute to, and lots of details on how to contribute to packages any time of year.
Software Review
Mark Padgham wrote about his recently rOpenSci reviewed package mapscanner: Rectifying Hand-Drawn Marks on Maps With the mapscanner Package. He discusses the motivation behind the package, and highlights three uses cases for mapscanner.
The following 19 works use/cite rOpenSci software:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Check out our guidance for taking over maintenance of a package.
We’ve had eight recent examples of maintainer transitions within rOpenSci:
We’ve got one package in need of a new maintainer:
We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.
Costa-Neto, G., Fritsche-Neto, R., & Crossa, J. (2020). Nonlinear kernels, dominance, and envirotyping data increase the accuracy of genome-based prediction in multi-environment trials. Heredity. https://doi.org/10.1038/s41437-020-00353-1 ↩
Ponce, M., & Sandhel, A. (2020). covid19. analytics: An R Package to Obtain, Analyze and Visualize Data from the Corona Virus Disease Pandemic. arXiv preprint arXiv:2009.01091 https://arxiv.org/pdf/2009.01091. ↩
Anderson, D. M., & Gillooly, J. F. (2020). Predicting egg size across temperatures in marine teleost fishes. Fish and Fisheries, 21(5), 1027–1033. https://doi.org/10.1111/faf.12486 ↩
Stevens, M. C., Chen, Y., Stringer, A., Clemmow, C., & Jones, L. A. (2020). Key factors driving obesity in the UK. http://london.gisruk.org/gisruk2020_proceedings/GISRUK2020_paper_17.pdf ↩
Schertler, A., Rabitsch, W., Moser, D., Wessely, J., & Essl, F. (2020). The potential current distribution of the coypu (Myocastor coypus) in Europe and climate change induced shifts in the near future. NeoBiota, 58, 129–160. https://doi.org/10.3897/neobiota.58.33118 ↩
Dion, M. L., Mitchell, S. M., & Sumner, J. L. (2020). Gender, seniority, and self-citation practices in political science. Scientometrics, 125(1), 1–28. https://doi.org/10.1007/s11192-020-03615-1 ↩
Bailey, T. W., Santos, A., Nascimento, N. C. de, Sivasankar, M. P., & Cox, A. (2020). RNA sequencing identifies transcriptional changes in the rabbit larynx in response to low humidity challenge. https://doi.org/10.21203/rs.3.rs-45442/v1 ↩
Tressel, L. G. (2020). A Morphological and Molecular Taxonomic Review of the Trifolium Depauperatum (Fabaceae) Species Complex (Doctoral dissertation, Miami University). https://bit.ly/2GRqint ↩
Guiterman, C. H., Lynch, A. M., & Axelson, J. N. (2020). dfoliatR: An R package for detection and analysis of insect defoliation signals in tree rings. Dendrochronologia, 63, 125750. https://doi.org/10.1016/j.dendro.2020.125750 ↩
Bauder, J. M., Allen, M. L., Ahlers, A. A., Benson, T. J., Miller, C. A., & Stodola, K. W. (2020). Identifying and Controlling for Variation in Canid Harvest Data. The Journal of Wildlife Management, 84(7), 1234–1245. https://doi.org/10.1002/jwmg.21919 ↩
Çetinkaya-Rundel, M., & Ellison, V. (2020). A Fresh Look at Introductory Data Science. Journal of Statistics Education, 1–11. https://doi.org/10.1080/10691898.2020.1804497 ↩
Duarte, S., Vieira, P. E., & Costa, F. O. (2020). Assessment of species gaps in DNA barcode libraries of non-indigenous species (NIS) occurring in European coastal regions. Metabarcoding and Metagenomics, 4. https://doi.org/10.3897/mbmg.4.55162 ↩
Dupont, G., Royle, J. A., Nawaz, M. A., & Sutherland, C. (2020). Optimal sampling design for spatial capture-recapture. https://doi.org/10.1101/2020.04.16.045740 ↩
Buil-Gil, D. (2020). Small Area Estimation for Crime Analysis. SocArXiv. https://doi.org/10.31235/osf.io/gtbyu ↩
Xaudiera, S., & Cardenal, A. S. (2020). Ibuprofen Narratives in Five European Countries During the COVID-19 Pandemic. Harvard Kennedy School Misinformation Review. https://doi.org/10.37016/mr-2020-029 ↩
Ferster, C., Laberee, K., Nelson, T., Thigpen, C., Simeone, M., & Winters, M. (2020). From advocacy to acceptance: Social media discussions of protected bike lane installations. Urban Studies, 004209802093825. https://doi.org/10.1177/0042098020938252 ↩
Sampath, W. W. H. A., Rathnayake, R. M. D. S., Yang, M., Zhang, W., & Mai, K. (2020). Roles of dietary taurine in fish nutrition. Marine Life Science & Technology. https://doi.org/10.1007/s42995-020-00051-1 ↩
Grenn, F. P., Kim, J. J., Makarious, M. B., Iwaki, H., Illarionova, A., … Brolin, K. (2020). The Parkinson’s Disease Genome‐Wide Association Study Locus Browser. Movement Disorders. https://doi.org/10.1002/mds.28197 ↩
Tang W. et al. (2020) Code Reusability and Transparency of Agent-Based Modeling: A Review from a Cyberinfrastructure Perspective. In: Tang W., Wang S. (eds) High Performance Computing for Geospatial Applications. Geotechnologies and the Environment, vol 23. Springer, Cham. https://doi.org/10.1007/978-3-030-47998-5_7 ↩
CRAN: GitHub:
v0.0.3) of medrxivr is on CRAN - access and search MedRxiv and BioRxiv preprint data. Checkout the docs to get started. This package recently went through rOpenSci software review. v0.7.1) of bomrang is on CRAN - Australian government Bureau of Meteorology (BOM) data. See the release notes for changes. Checkout the docs to get started. v0.5.1) of emld is on CRAN - ecological metadata as linked data. See the release notes for changes. Checkout the docs to get started. v0.2.0) of opencv is on CRAN - bindings to the OpenCV computer vision library. See the release notes for changes. Checkout the docs to get started. v2.0.0) of nasapower is on CRAN - NASA POWER API Client. See the release notes for changes. Checkout the docs to get started. v0.2.0) of gutenbergr is on CRAN - Download and process public domain works from Project Gutenberg. See the release notes for changes. Checkout the vignette to get started. v2.1.2) of GSODR is on CRAN - Global Surface Summary of the Day (GSOD) Weather Data from R. See the release notes for changes. Checkout the docs to get started. v2.0.3) of MODIStsp is on CRAN - Automate Download and Preprocessing of MODIS Land Products Data. See the release notes for changes. Checkout the docs to get started. v0.0.6) of arkdb is on CRAN - archive and unarchive databases as flat text files. See the release notes for changes. Checkout the docs to get started. v1.0.1) of rppo is on CRAN - access the Global Plant Phenology Data portal. See the release notes for changes. Checkout the docs to get started. v0.9.98) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started. v1.1) of tradestatistics is on CRAN - open trade statistics api wrapper and utility program. See the release notes for changes. Checkout the docs to get started. v3.0.0) of rdataretriever is on CRAN - R interface to the Data Retriever. See the release notes for changes. Checkout the docs to get started. We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following two packages were recently approved:
![](\"../assets/img/treedatatable-logo.png\"){kind=logo}
![](\"../assets/img/medrxivr-logo.png\"){kind=logo}
Software Review:
April Wright, Christian Román-Palacios, and Josef Uyeda wrote about their recently rOpenSci reviewed package treedata.table: The treedata.table Package. They discuss how the package came about, why you should use the packag and a bit of high level talk on what can be done with the package.
The following 18 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
Four new use cases were shared in the forum over the past two weeks since our last newsletter:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Check out our guidance for taking over maintenance of a package.
We’ve had eight recent examples of maintainer transitions within rOpenSci:
We’ve got one package in need of a new maintainer:
We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.
Ehlers, M., Nold, J., Kuhn, M., Klingelhöfer-Jens, M., & Lonsdorf, T. (2020). Natural variations in brain morphology do not account for inter-individual differences in defensive responding during fear acquisition training and extinction. https://psyarxiv.com/q2kyf/download?format=pdf ↩
Jerabek M., Kubat J., Fabera V. (2020) Method to Comparison of Cities. In: Knapcikova L., Balog M., Peraković D., Periša M. (eds) New Approaches in Management of Smart Manufacturing Systems. EAI/Springer Innovations in Communication and Computing. Springer, Cham. https://doi.org/10.1007/978-3-030-40176-4_7 ↩
Westfall J. (2020) R Anywhere. In: Practical R 4. Apress, Berkeley, CA. https://doi.org/10.1007/978-1-4842-5946-7_8 ↩
Arranz, V., Pearman, W. S., Aguirre, J. D., & Liggins, L. (2020). MARES, a replicable pipeline and curated reference database for marine eukaryote metabarcoding. Scientific Data, 7(1). https://doi.org/10.1038/s41597-020-0549-9 ↩
Leonard, S. P. (2020). Engineering the gut microbiome of honey bees (Doctoral dissertation). https://bit.ly/3cFfZhT ↩
LeBeau, B. C., & Aloe, A. M. (2020). Evolution of Statistical Software and Quantitative Methods. https://doi.org/10.17077/pp.005273 ↩
van Wieringen, W. N., & Binder, H. (2020). Transfer learning of regression models from a sequence of datasets by penalized estimation. arXiv preprint arXiv:2007.02117. https://arxiv.org/pdf/2007.02117 ↩
Hock, M., Hofmann, R., Essl, F., Pyšek, P., Bruelheide, H., & Erfmeier, A. (2020). Native distribution characteristics rather than functional traits explain preadaptation of invasive species to high‐UV‐B environments. Diversity and Distributions. https://doi.org/10.1111/ddi.13113 ↩
Cagua, F. (2020). Plant–pollinator communities: environmental gradients, trade-offs, and controllability. PhD Thesis. https://bit.ly/3kZDHrZ ↩
Álvarez-Noriega, M., Burgess, S. C., Byers, J. E., Pringle, J. M., Wares, J. P., & Marshall, D. J. (2020). Global biogeography of marine dispersal potential. Nature Ecology & Evolution, 4(9), 1196–1203. https://doi.org/10.1038/s41559-020-1238-y ↩
Anton, C. (2020). The Demography and Comparative Ethology of Top Predators in a Multi-Carnivore System (Doctoral dissertation, UC Santa Cruz). https://escholarship.org/content/qt3xd9379b/qt3xd9379b.pdf ↩
Berkel, C., & Cacan, E. (2020). GAB2 and GAB3 are expressed in a tumor stage-, grade- and histotype-dependent manner and are associated with shorter progression-free survival in ovarian cancer. Journal of Cell Communication and Signaling. https://doi.org/10.1007/s12079-020-00582-3 ↩
Mallet, M. D. (2020). Meteorological normalisation of PM10 using machine learning reveals distinct increases of nearby source emissions in the Australian mining town of Moranbah. Atmospheric Pollution Research. https://doi.org/10.1016/j.apr.2020.08.001 ↩
Presa-Reyes, M., Bogosian, B., Schonhoff, B., Jerauld, C., Moreyra, C., Gardinali, P., & Chen, S. C. A Water Quality Research Platform for the Near-real-time Buoy Sensor Data. https://users.cs.fiu.edu/~chens/PDF/IRI20_Buoy.pdf ↩
Dogucu, M., & Çetinkaya-Rundel, M. (2020). Web Scraping in the Statistics and Data Science Curriculum: Challenges and Opportunities. Journal of Statistics Education, 1–11. https://doi.org/10.1080/10691898.2020.1787116 ↩
Scott, T. A., Ulibarri, N., & Perez Figueroa, O. (2020). NEPA and National Trends in Federal Infrastructure Siting in the United States. Review of Policy Research. https://doi.org/10.1111/ropr.12399 ↩
Waldock, C. A., De Palma, A., Borges, P. A. V., & Purvis, A. (2020). Insect occurrence in agricultural land‐uses depends on realized niche and geographic range properties. Ecography. https://doi.org/10.1111/ecog.05162 ↩
Saleh, S. N., Lehmann, C. U., McDonald, S. A., Basit, M. A., & Medford, R. J. (2020). Understanding public perception of coronavirus disease 2019 (COVID-19) social distancing on Twitter. Infection Control & Hospital Epidemiology, 1–8. https://doi.org/10.1017/ice.2020.406 ↩
Our own community manager Stefanie Butland, and one of our software review editors Brooke Anderson, are remotely speaking at an R-Ladies East Lansing meetup on Thursday, October 22nd: rOpenSci - open tools for open science. If you’d like to attend, see “Who could join?” on the R-Ladies East Lansing page.
CRAN: GitHub:
v0.2.0) of rbace is on CRAN - a client for interacting with the Bielefeld Academic Search Engine API. See the docs to get started. v3.3.0) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the occurrence manual to get started. v0.3.0) of pubchunks is on CRAN - Fetch Sections of XML Scholarly Articles. See the release notes for changes. Checkout the README to get started. v0.7.2) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. v0.7.13) of robotstxt is on CRAN - robots.txt parser and Webbot/Spider/Crawler permissions checker. See the release notes for changes. Checkout the docs to get started. v2.0.2) of MODIStsp is on CRAN - Automate Download and Preprocessing of MODIS Land Products Data. See the release notes for changes. Checkout the docs to get started. v0.4.0) of weathercan is on CRAN - Download weather data from the Environment and Climate Change Canada website. See the release notes for changes. Checkout the docs to get started. v3.2-3) of clifro is on CRAN - easily download and visualise climate data from CliFlo. See the release notes for changes. Checkout the docs to get started. v0.1.5) of virtuoso is on CRAN - interface to Virtuoso using ODBC. See the release notes for changes. Checkout the docs to get started. We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
No new submissions or approved submissions.
The following 19 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
A new use case was shared in the forum over the past two weeks since our last newsletter:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Check out our guidance for taking over maintenance of a package.
We’ve had eight recent examples of maintainer transitions within rOpenSci:
We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.
Li, D., Olden, J. D., Lockwood, J. L., Record, S., McKinney, M. L., & Baiser, B. (2020). Changes in taxonomic and phylogenetic diversity in the Anthropocene. Proceedings of the Royal Society B: Biological Sciences, 287(1929), 20200777. https://doi.org/10.1098/rspb.2020.0777 ↩
James, S., Pagliari, S., & Young, K. L. (2020). The internationalization of European financial networks: a quantitative text analysis of EU consultation responses. Review of International Political Economy, 1–28. https://doi.org/10.1080/09692290.2020.1779781 ↩
Drost, H.-G. (2020). LTRpred: de novo annotation of intact retrotransposons. Journal of Open Source Software, 5(50), 2170. https://doi.org/10.21105/joss.02170 ↩
Granados, J. E., Ros-Candeira, A., Pérez-Luque, A. J., Moreno-Llorca, R., Cano-Manuel, F. J., Fandos, P., … Zamora, R. (2020). Long-term monitoring of the Iberian ibex population in the Sierra Nevada of the southeast Iberian Peninsula. Scientific Data, 7(1). https://doi.org/10.1038/s41597-020-0544-1 ↩
Brazeau, N. (2020). The Molecular, Spatial, and Genetic Epidemiology of Malaria in the Democratic Republic of the Congo. https://cdr.lib.unc.edu/downloads/7s75dj87g ↩
Pacifico, R., Almeda, F., Frota, A., & Fidanza, K. (2020). Areas of endemism on Brazilian mountaintops revealed by taxonomically verified records of Microlicieae (Melastomataceae). Phytotaxa, 450(2), 119–148. https://doi.org/10.11646/phytotaxa.450.2.1 ↩
Hanes, C., Wotton, M., Woolford, D. G., Martell, D. L., & Flannigan, M. (2020). Preceding Fall Drought Conditions and Overwinter Precipitation Effects on Spring Wildland Fire Activity in Canada. Fire, 3(2), 24. https://www.mdpi.com/2571-6255/3/2/24/pdf ↩
Burda, P.-C., Crosskey, T., Lauk, K., Zurborg, A., Söhnchen, C., Liffner, B., … Gilberger, T.-W. (2020). Structure-Based Identification and Functional Characterization of a Lipocalin in the Malaria Parasite Plasmodium falciparum. Cell Reports, 31(12), 107817. https://doi.org/10.1016/j.celrep.2020.107817 ↩
Corput, D. V. D. (2020). Locked in Syndrome Machine Learning Classification using Sentence Comprehension EEG Data. arXiv preprint arXiv:2006.12336 https://arxiv.org/pdf/2006.12336.pdf ↩
Stephens, M. (2020). A geospatial infodemic: Mapping Twitter conspiracy theories of COVID-19. Dialogues in Human Geography, 10(2), 276–281. https://doi.org/10.1177/2043820620935683 ↩
Green, J., Edgerton, J., Naftel, D., Shoub, K., & Cranmer, S. J. (2020). Elusive consensus: Polarization in elite communication on the COVID-19 pandemic. Science Advances, 6(28), eabc2717. https://doi.org/10.1126/sciadv.abc2717 ↩
Jayawardhana, W. G. N. N., & Chathurange, V. M. I. (2020). Investigate the sensitivity of the satellite-based agricultural drought indices to monitor the drought condition of paddy and introduction to enhanced multi-temporal agricultural drought indices. J Remote Sens GIS, 9, 271. https://bit.ly/2RoRprZ ↩
Da Silva, R. G., Ribeiro, M. H. D. M., Mariani, V. C., & Coelho, L. dos S. (2020). Forecasting Brazilian and American COVID-19 cases based on artificial intelligence coupled with climatic exogenous variables. Chaos, Solitons & Fractals, 139, 110027. https://doi.org/10.1016/j.chaos.2020.110027 ↩
Sacchi, R., Cancian, S., Ghia, D., Fea, G., & Coladonato, A. (2020). Colour variation in signal crayfish Pacifastacus leniusculus. Current Zoology. https://academic.oup.com/cz/advance-article/doi/10.1093/cz/zoaa031/5865267 ↩
Charalampopoulos, I. (2020). The R Language as a Tool for Biometeorological Research. Atmosphere, 11(7), 682. https://doi.org/10.3390/atmos11070682 ↩
Oh, S., Yeom, J., Cho, H. J., Kim, J.-H., Yoon, S.-J., Kim, H., … Kim, H. S. (2020). Integrated pharmaco-proteogenomics defines two subgroups in isocitrate dehydrogenase wild-type glioblastoma with prognostic and therapeutic opportunities. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-17139-y ↩
Sun, M., Folk, R. A., Gitzendanner, M. A., Soltis, P. S., Chen, Z., Soltis, D. E., & Guralnick, R. P. (2020). Recent accelerated diversification in rosids occurred outside the tropics. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-17116-5 ↩
Griffiths, D. (2020). Foraging habitat determines predator–prey size relationships in marine fishes. Journal of Fish Biology. https://doi.org/10.1111/jfb.14451 ↩
Kurose, D., Pollard, K. M., & Ellison, C. A. (2020). Chloroplast DNA analysis of the invasive weed, Himalayan balsam (Impatiens glandulifera), in the British Isles. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-67871-0 ↩
Contributing Guide Release 🚀
https://contributing.ropensci.org/
The purpose of the guide is to welcome you to rOpenSci and help you recognize yourself as a potential contributor. It will help you figure out what you might gain by giving your time, expertise, and experience; match your needs with things that will help rOpenSci’s mission; and connect you with resources to help you along the way. Is there something you might like to contribute that isn’t addressed there? Open an issue in the GitHub repository for the Guide.
CRAN: GitHub:
v3.2-3) of clifro is on CRAN - easily download and visualise climate data from CliFlo. See the release notes for changes. Checkout the docs to get started. v2.0-17) of CoordinateCleaner is on CRAN - automated cleaning of occurrence records from biological collections. See the release notes for changes. Checkout the docs to get started. v0.4.0) of rsnps is on CRAN - fetch SNP (Single-Nucleotide Polymorphism) data from the web. See the release notes for changes. Checkout the docs to get started. v0.7.0) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. v0.5.0) of traits is on CRAN - species trait data from around the web. See the release notes for changes. Checkout the docs to get started. v0.3.0) of ccafs is on CRAN - client for Climate Change, Agriculture, & Food Security (CCAFS) General Circulation Models. See the release notes for changes. Checkout the docs to get started. v0.7.4) of DataSpaceR is on CRAN - interface to the CAVD DataSpace. See the release notes for changes. Checkout the docs to get started. v1.2.0) of dbparser is on CRAN - DrugBank database XML parser. See the release notes for changes. Checkout the docs to get started. v7.12.5) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started. v0.2.2) of taxizedb is on CRAN - tools for working with taxonomic databases. See the release notes for changes. Checkout the docs to get started. v1.3.1) of writexl is on CRAN - a portable, light-weight data frame to xlsx exporter. See the release notes for changes. Checkout the docs to get started. We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
No new submissions or approved submissions.
It’s time for another installment of … 2 Months in 2 Minutes - rOpenSci News, February 2020 - if you want a brief summary of the last 2 months of these newsletters, these blog posts are for you (written by Stefanie Butland)
Software Review:
Jonathan Keane wrote about their recently rOpenSci reviewed package dittodb: Developing dittodb. Jonathan discusses the motivation behind the package, some of the technical challenges, and the story behind the name of the package.
Scott Chamberlain wrote a post on Scientific Name Parsing: rgnparser and namext, covering the rgnparser and namext packages.
The following 18 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
A new use case was shared in the forum over the past two weeks since our last newsletter:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Check out our guidance for taking over maintenance of a package.
We’ve had eight recent examples of maintainer transitions within rOpenSci:
We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.
Ordynets, A., Liebisch, R., Lysenko, L., Scherf, D., Volobuev, S., Saitta, A., … Langer, E. (2020). Morphologically similar but not closely related: the long-spored species of Subulicystidium (Trechisporales, Basidiomycota). Mycological Progress, 19(7), 691–703. https://doi.org/10.1007/s11557-020-01587-3 ↩
Ye, J. (2020). Independent and dependent possessive person forms. Studies in Language, 44(2), 363–406. https://doi.org/10.1075/sl.19020.ye ↩
Monaco, C. J., Bradshaw, C. J. A., Booth, D. J., Gillanders, B. M., Schoeman, D. S., & Nagelkerken, I. (2020). Dietary generalism accelerates arrival and persistence of coral‐reef fishes in their novel ranges under climate change. Global Change Biology. https://doi.org/10.1111/gcb.15221 ↩
Tennant, W. S. D., Tildesley, M. J., Spencer, S. E. F., & Keeling, M. J. (2020). Climate drivers of plague epidemiology in British India, 1898–1949. Proceedings of the Royal Society B: Biological Sciences, 287(1928), 20200538. https://doi.org/10.1098/rspb.2020.0538 ↩
Runge, C. A., Hausner, V. H., Daigle, R. M., & Monz, C. A. (2020). Pan-Arctic analysis of cultural ecosystem services using social media and automated content analysis. Environmental Research Communications, 2(7), 075001. https://doi.org/10.1088/2515-7620/ab9c33 ↩
Swetnam, D. M., Stuart, J. B., Young, K., Maharaj, P. D., Fang, Y., Garcia, S., … Coffey, L. L. (2020). Movement of St. Louis encephalitis virus in the Western United States, 2014- 2018. PLOS Neglected Tropical Diseases, 14(6), e0008343. https://doi.org/10.1371/journal.pntd.0008343 ↩
Walker, P. G. T., Whittaker, C., Watson, O. J., Baguelin, M., Winskill, P., Hamlet, A., … Ghani, A. C. (2020). The impact of COVID-19 and strategies for mitigation and suppression in low- and middle-income countries. Science, eabc0035. https://doi.org/10.1126/science.abc0035 ↩
McDonald, S. (2020). Applying Geographic Information Systems to the Study of Honey Bee Diseases and Pests (Doctoral dissertation). https://bit.ly/34Ox33c ↩
Ficcadenti, V., Cerqueti, R., Ausloos, M., & Dhesi, G. (2020). Words ranking and Hirsch index for identifying the core of the hapaxes in political texts. Journal of Informetrics, 14(3), 101054. https://doi.org/10.1016/j.joi.2020.101054 ↩
Hierink, F., Bolon, I., Durso, A. M., Ruiz de Castañeda, R., Zambrana-Torrelio, C., Eskew, E. A., & Ray, N. (2020). Forty-four years of global trade in CITES-listed snakes: Trends and implications for conservation and public health. Biological Conservation, 248, 108601. https://doi.org/10.1016/j.biocon.2020.108601 ↩
Pal Negi, A., Singh, R., Sharma, A., & Negi, V. S. (2020). Insights into high mobility group A (HMGA) proteins from Poaceae family: An in silico approach for studying homologs. Computational Biology and Chemistry, 87, 107306. https://doi.org/10.1016/j.compbiolchem.2020.107306 ↩
Puerta, P., Laguna, L., Vidal, L., Ares, G., Fiszman, S., & Tárrega, A. (2020). Co-occurrence networks of Twitter content after manual or automatic processing. A case-study on “gluten-free.” Food Quality and Preference, 86, 103993. https://doi.org/10.1016/j.foodqual.2020.103993 ↩
Anton, C. B., Smith, D. W., Suraci, J. P., Stahler, D. R., Duane, T. P., & Wilmers, C. C. (2020). Gray wolf habitat use in response to visitor activity along roadways in Yellowstone National Park. Ecosphere, 11(6). https://doi.org/10.1002/ecs2.3164 ↩
Loewen, C. J. G., Strecker, A. L., Gilbert, B., & Jackson, D. A. (2020). Climate warming moderates the impacts of introduced sportfish on multiple dimensions of prey biodiversity. Global Change Biology, 26(9), 4937–4951. https://doi.org/10.1111/gcb.15225 ↩
Siregar, E., & Prawisudatama, A. Improving data literacy using liteRate: an R Shiny Apps for visualizing and exploring data published on BPS-Statistics Indonesia’s Website https://bit.ly/2ELTyuZ ↩
Bisbee, J., & Honig, D. (2020). Flight to Safety: 2020 Democratic Primary Election Results and COVID-19. Covid Economics, 3(10), 54-84. https://bit.ly/2YRiWWP ↩
Hobert, A., Jahn, N., Mayr, P., Schmidt, B., & Taubert, N. C. (2020). Open Access Uptake in Germany 2010-18: Adoption in a diverse research landscape. https://bit.ly/3bt1LjP ↩
Webb, T. J., Lines, A., & Howarth, L. M. (2020). Occupancy‐derived thermal affinities reflect known physiological thermal limits of marine species. Ecology and Evolution, 10(14), 7050–7061. https://doi.org/10.1002/ece3.6407 ↩
CRAN: GitHub:
v0.2.0) of taxizedb is on CRAN - tools for working with taxonomic databases. See the release notes for changes. Checkout the docs to get started. v2.1.4) of babette is on CRAN - control BEAST2 from R. See the release notes for changes. Checkout the docs to get started. v0.4.0) of finch is on CRAN - parse Darwin Core files. See the release notes for changes. Checkout the README to get started. v2.1) of mauricer is on CRAN - install BEAST2 packages. See the release notes for changes. Checkout the docs to get started. v2.1.3) of beastier is on CRAN - Provides a way to call BEAST2 from R. See the release notes for changes. Checkout the docs to get started. v2.3.7) of beautier is on CRAN - create BEAST2 input files programmatically. See the release notes for changes. Checkout the docs to get started. v2.2.0) of ijtiff is on CRAN - comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started. v1.3.3) of UCSCXenaTools is on CRAN - download and explore datasets from UCSC Xena data hubs. See the release notes for changes. Checkout the docs to get started. v1.1-3) of suppdata is on CRAN - downloading supplementary data from published manuscripts. See the release notes for changes. Checkout the vignette to get started. We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
No new submissions or approved submissions.
The following 22 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
A new use case was shared in the forum over the past two weeks since our last newsletter:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Check out our guidance for taking over maintenance of a package.
We’ve had nine recent examples of maintainer transitions within rOpenSci:
We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.
Connors, B., Malick, M. J., Ruggerone, G. T., Rand, P., Adkison, M., Irvine, J. R., … Gorman, K. (2020). Climate and competition influence sockeye salmon population dynamics across the Northeast Pacific Ocean. Canadian Journal of Fisheries and Aquatic Sciences, 77(6), 943–949. https://www.nrcresearchpress.com/doi/10.1139/cjfas-2019-0422 ↩
Hesselbarth, M. H. 2020. Analysing and modelling spatial patterns to infer the influence of environmental heterogeneity using point pattern analysis, individual-based simulation modelling and landscape metrics. Dissertation https://bit.ly/2E0yuAx ↩
Geller, J., Davis, S. D., & Peterson, D. (2020, May 23). Sans forgetica is not desirable for learning. https://doi.org/10.31234/osf.io/ku5bz ↩
Biber‐Freudenberger, L., Ergeneman, C., Förster, J. J., Dietz, T., & Börner, J. (2020). Bioeconomy futures: Expectation patterns of scientists and practitioners on the sustainability of bio‐based transformation. Sustainable Development. https://doi.org/10.1002/sd.2072 ↩
Siqueira, A. C., Morais, R. A., Bellwood, D. R., & Cowman, P. F. (2020). Trophic innovations fuel reef fish diversification. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-16498-w ↩
D’Orazio, M., Bernardini, G., & Quagliarini, E. (2020). Sustainable and resilient strategies for touristic cities against COVID-19: an agent-based approach. arXiv preprint arXiv:2005.12547. https://arxiv.org/pdf/2005.12547.pdf ↩
Stringham, O., Toomes, A., Kanishka, A. M., Mitchell, L., Heinrich, S., Ross, J. V., & Cassey, P. (2020). A guide to using the Internet to monitor and quantify the wildlife trade. https://ecoevorxiv.org/5yzw9/download?format=pdf ↩
Morselli, D., Passini, S., & McGarty, C. (2020). Sos Venezuela: an analysis of the anti-Maduro protest movements using Twitter. Social Movement Studies, 1–22. https://doi.org/10.1080/14742837.2020.1770072 ↩
Vogler, D., & Schäfer, M. S. (2020). Growing Influence of University PR on Science News Coverage? A Longitudinal Automated Content Analysis of University Media Releases and Newspaper Coverage in Switzerland, 2003‒2017. International Journal of Communication, 14, 22. https://ijoc.org/index.php/ijoc/article/download/13498/3113 ↩
Szöcs, E., Stirling, T., Scott, E. R., Scharmüller, A., & Schäfer, R. B. (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(1), 1-17. https://www.jstatsoft.org/article/view/v093i13/v93i13.pdf ↩
Manning, F., Curtis, P. J., Walker, I., & Pither, J. (2020, June 2). An experimental test of the capacity for long-distance dispersal of freshwater diatoms adhering to waterfowl plumage. https://doi.org/10.32942/osf.io/h97pw ↩
Greco, F., & La Rocca, G. (2020). The Topics-scape of the Pandemic Crisis: The Italian Sentiment on Political Leaders. Culture e Studi del Sociale, 5(1, Special), 335-346. http://www.cussoc.it/index.php/journal/article/view/134 ↩
Fernández-Ruiz, N., & Estrada-Peña, A. (2020). Could climate trends disrupt the contact rates between Ixodes ricinus (Acari, Ixodidae) and the reservoirs of Borrelia burgdorferi s.l.? PLOS ONE, 15(5), e0233771. https://doi.org/10.1371/journal.pone.0233771 ↩
Santana, V. M., Alday, J. G., Adamo, I., Alloza, J. A., & Baeza, M. J. (2020). Climate, and not fire, drives the phylogenetic clustering of species with hard-coated seeds in Mediterranean Basin communities. Perspectives in Plant Ecology, Evolution and Systematics, 45, 125545. https://doi.org/10.1016/j.ppees.2020.125545 ↩
Sales, L., Culot, L., & Pires, M. M. (2020). Climate niche mismatch and the collapse of primate seed dispersal services in the Amazon. Biological Conservation, 247, 108628. https://doi.org/10.1016/j.biocon.2020.108628 ↩
Barrios‐O’Neill, D. (2020). Focus and social contagion of environmental organization advocacy on Twitter. Conservation Biology. https://doi.org/10.1111/cobi.13564 ↩
Gaynor, M. L., Fu, C., Gao, L., Lu, L., Soltis, D. E., & Soltis, P. S. (2020). Biogeography and ecological niche evolution in Diapensiaceae inferred from phylogenetic analysis. Journal of Systematics and Evolution. https://doi.org/10.1111/jse.12646 ↩
Liu, L., Huang, J., Xiong, Q., Zhang, H., Song, P., Huang, Y., … Wang, X. (2020). Optimal MODIS data processing for accurate multi-year paddy rice area mapping in China. GIScience & Remote Sensing, 57(5), 687–703. https://doi.org/10.1080/15481603.2020.1773012 ↩
Estrada-Peña, A., Nava, S., Tarragona, E., de la Fuente, J., & Guglielmone, A. A. (2020). A community approach to the Neotropical ticks-hosts interactions. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-66400-3 ↩
Trinka, J., Haghbin, H., & Maadooliat, M. (2020). Multivariate Functional Singular Spectrum Analysis Over Different Dimensional Domains. arXiv preprint arXiv:2006.03933. https://arxiv.org/pdf/2006.03933 ↩
McKnelly, K. J., Howitz, W. J., Lam, S., & Link, R. D. (2020). Extraction on Paper Activity: An Active Learning Technique to Facilitate Student Understanding of Liquid–Liquid Extraction. Journal of Chemical Education, 97(7), 1960–1965. https://doi.org/10.1021/acs.jchemed.9b00975 ↩
Davis, Z. (2020). Leaf the kids outdoors: approaches and enquiries in quantifying natural environments for health (Doctoral dissertation, University of British Columbia). https://open.library.ubc.ca/collections/ubctheses/24/items/1.0391841 ↩
CRAN: GitHub:
v0.1.0) of dittodb is on CRAN - a test environment for database requests. It went through rOpenSci software review recently - check out the reviews. Checkout the docs to get started. v1.1-3) of suppdata is on CRAN - downloading supplementary data from published manuscripts. See the release notes for changes. Checkout the vignette to get started. v1.1.0) of spocc is on CRAN - an interface to many species occurrence data sources. See the release notes for changes. Checkout the docs to get started. v0.5.0) of ckanr is on CRAN - client for the CKAN API. See the release notes for changes. Checkout the docs to get started. v1.0.0) of crul is on CRAN - an R6 based HTTP client for R made for developers. See the release notes for changes. Checkout the docs to get started. v0.5.0) of mapr is on CRAN - visualize species occurrence data. See the release notes for changes. Checkout the vignette to get started. v0.9.0) of gistr is on CRAN - work with GitHub Gists. See the release notes for changes. Checkout the docs to get started. v0.2.10) of ropenaq is on CRAN - air quality data from the open data platform OpenAQ. See the release notes for changes. Checkout the docs to get started. v0.7.0) of paleobioDB is on CRAN - download and process data from the Paleobiology database. See the release notes for changes. Checkout the docs to get started. v0.7.8) of robotstxt is on CRAN - robots.txt parser and Webbot/Spider/Crawler permissions checker. See the release notes for changes. Checkout the docs to get started. v2.1.2) of ijtiff is on CRAN - comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started. v2.0.2/v2.0.3) of EML are on CRAN - read and write ecological metadata language files. See the release notes for changes. Checkout the docs to get started. v3.2.0) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the occurrence manual to get started. v1.3.0) of credentials is on CRAN - tools for managing ssh and git credentials. See the release notes for changes. Checkout the docs to get started. v0.7.0) of ssh is on CRAN - secure shell (SSH) client for R. See the release notes for changes. Checkout the vignette to get started. Software review is now accepting submissions again.
We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
No new submissions or approved submissions.
The following 20 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
A few new use cases were shared in the forum over the past two weeks since our last newsletter:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Check out our guidance for taking over maintenance of a package.
We’ve had nine recent examples of maintainer transitions within rOpenSci:
We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.
Scharmüller, A., Schreiner, V. C., & Schäfer, R. B. (2020). Standartox: Standardizing Toxicity Data. Data, 5(2), 46. https://doi.org/10.3390/data5020046 ↩
Nguyen, C. T., Nguyen, D. T. H., & Phan, D. K. (2020). Factors affecting urban electricity consumption: a case study in the Bangkok Metropolitan Area using an integrated approach of earth observation data and data analysis. Environmental Science and Pollution Research. https://doi.org/10.1007/s11356-020-09157-6 ↩
Upadhya, A., Agrawal, P., Vakacherla, S., & Kushwaha, M. (2020). mmaqshiny v1.0: R-Shiny package to explore Air-Quality Mobile-Monitoring data. Journal of Open Source Software, 5(50), 2250. https://doi.org/10.21105/joss.02250 ↩
Rahman, M. M., Ali, G. G., Li, X. J., Paul, K. C., & Chong, P. H. (2020). Twitter and Census Data Analytics to Explore Socioeconomic Factors for Post-COVID-19 Reopening Sentiment. Nawaz and Li, Xue Jun and Paul, Kamal Chandra and Chong, Peter HJ, Twitter and Census Data Analytics to Explore Socioeconomic Factors for Post-COVID-19 Reopening Sentiment (June 30, 2020). https://arxiv.org/pdf/2007.00054.pdf ↩
Colling LJ, Szűcs D, De Marco D, et.al., A multilab registered replication of the attentional SNARC effect, Advances in Methods and Practices in Psychological Science (Forthcoming) https://dspace.stir.ac.uk/retrieve/cb22b749-5134-44ec-ae5b-7f66efbad76f/Colling%20et%20al_AMPPS_SNARC.pdf ↩
Lam, K.-L., Cheng, W.-Y., Su, Y., Li, X., Wu, X., Wong, K.-H., … Cheung, P. C.-K. (2020). Use of random forest analysis to quantify the importance of the structural characteristics of beta-glucans for prebiotic development. Food Hydrocolloids, 108, 106001. https://doi.org/10.1016/j.foodhyd.2020.106001 ↩
Deconinck, D., Volckaert, F. A. M., Hostens, K., Panicz, R., Eljasik, P., Faria, M., … Derycke, S. (2020). A high-quality genetic reference database for European commercial fishes reveals substitution fraud of processed Atlantic cod (Gadus morhua) and common sole (Solea solea) at different steps in the Belgian supply chain. Food and Chemical Toxicology, 141, 111417. https://doi.org/10.1016/j.fct.2020.111417 ↩
Bohora Schlickmann, M., da Silva, A. C., de Oliveira, L. M., Oliveira Matteucci, D., Domingos Machado, F., Cuchi, T., … Higuchi, P. (2020). Specific leaf area is a potential indicator of tree species sensitive to future climate change in the mixed Subtropical Forests of southern Brazil. Ecological Indicators, 116, 106477. https://doi.org/10.1016/j.ecolind.2020.106477 ↩
Shrestha, R. K., & Shrestha, R. (2020). Group segmentation and heterogeneity in the choice of cooking fuels in post-earthquake Nepal. arXiv preprint arXiv:2005.09616. https://arxiv.org/pdf/2005.09616.pdf ↩
Crowley, D., Becker, D., Washburne, A., & Plowright, R. (2020). Identifying Suspect Bat Reservoirs of Emerging Infections. Vaccines, 8(2), 228. https://doi.org/10.3390/vaccines8020228 ↩
Joyce, E., Thiele, K., Slik, F., & Crayn, D. (2020). Checklist of the vascular flora of the Sunda-Sahul Convergence Zone. Biodiversity Data Journal, 8. https://doi.org/10.3897/bdj.8.e51094 ↩
Camacho, K. (2020). Sentiment mapping: Point pattern analysis of sentiment classified twitter data (Order No. 27962629). Available from ProQuest Dissertations & Theses A&I; ProQuest Dissertations & Theses Global. (2404054000). Retrieved from https://search.proquest.com/docview/2404054000?accountid=14496 ↩
Haußner, S., & Klika, C. (2020). Who Is Connected to Whom? A Twitter-Based Network Analysis of Members of the European Parliament Elected in 2019. In Die Europawahl 2019 (pp. 423-435). Springer VS, Wiesbaden. https://doi.org/10.1007/978-3-658-29277-5_34 ↩
Petersen, T. K., Speed, J. D. M., Grøtan, V., & Austrheim, G. (2020). Urban aliens and threatened near-naturals: Land-cover affects the species richness of alien- and threatened species in an urban-rural setting. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-65459-2 ↩
Lindberg, C. L., Hanslin, H. M., Schubert, M., Marcussen, T., Trevaskis, B., Preston, J. C., & Fjellheim, S. (2020). Increased above‐ground resource allocation is a likely precursor for independent evolutionary origins of annuality in the Pooideae grass subfamily. New Phytologist. https://doi.org/10.1111/nph.16666 ↩
Donnellan, E., Aslan, S., Fastrich, G. M., & Murayama, K. (2020, May 20). How are Curiosity and Interest Different? Naïve Bayes Classification of People’s Naïve Belief. https://doi.org/10.31234/osf.io/697gk ↩
Gold, Z. J. (2020). Design and Implementation of Environmental DNA Metabarcoding Methods for Monitoring the Southern California Marine Protected Area Network (Doctoral dissertation, UCLA) https://escholarship.org/content/qt7zf5g0cb/qt7zf5g0cb.pdf ↩
Lenoir, J., Bertrand, R., Comte, L., Bourgeaud, L., Hattab, T., Murienne, J., & Grenouillet, G. (2020). Species better track climate warming in the oceans than on land. Nature Ecology & Evolution. https://doi.org/10.1038/s41559-020-1198-2 ↩
De Almeida Monteiro Melo Ferraz, M., Fujihara, M., Nagashima, J. B., Noonan, M. J., Inoue-Murayama, M., & Songsasen, N. (2020). Follicular extracellular vesicles enhance meiotic resumption of domestic cat vitrified oocytes. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-65497-w ↩
Joo, R., Picardi, S., Boone, M. E., Clay, T. A., Patrick, S. C., Romero-Romero, V. S., & Basille, M. (2020). A decade of movement ecology. arXiv preprint arXiv:2006.00110 https://arxiv.org/pdf/2006.00110.pdf ↩
CRAN: GitHub:
v0.1.9) of codemetar is on CRAN - Generate codemeta metadata for R packages. See the release notes for changes. Checkout the docs to get started. v1.3.2) of UCSCXenaTools is on CRAN - download and explore datasets from UCSC Xena data hubs. See the release notes for changes. Checkout the docs to get started. v0.1.2) of chirps is on CRAN - client for the Climate Hazards Group InfraRed Precipitation with Station Data. See the release notes for changes. Checkout the docs to get started. v0.5.0) of emld is on CRAN - ecological metadata as linked data. See the release notes for changes. Checkout the docs to get started. v1.1.0) of rnoaa is on CRAN - NOAA Weather Data from R. See the release notes for changes. Checkout the docs to get started. v0.6.2) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. v0.4.2) of worrms is on CRAN - client for World Register of Marine Species. See the release notes for changes. Checkout the docs to get started. v0.5.0) of iheatmapr is on CRAN - Interactive and complex heatmaps. See the release notes for changes. Checkout the docs to get started. v0.4.0) of rcoreoa is on CRAN - client for CORE https://core.ac.uk/. See the release notes for changes. Checkout the docs to get started. Software review is now accepting submissions again.
We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following two packages were recently submitted:
The following 30 works use/cite rOpenSci software:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Check out our guidance for taking over maintenance of a package.
We’ve had nine recent examples of maintainer transitions within rOpenSci:
We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.
Adams, R. I., Bhangar, S., Dannemiller, K. C., Eisen, J. A., Fierer, N., Gilbert, J. A., … Bibby, K. (2016). Ten questions concerning the microbiomes of buildings. Building and Environment, 109, 224–234. https://doi.org/10.1016/j.buildenv.2016.09.001 ↩
Dunnett, S., Sorichetta, A., Taylor, G., & Eigenbrod, F. (2020). Harmonised global datasets of wind and solar farm locations and power. Scientific Data, 7(1). https://doi.org/10.1038/s41597-020-0469-8 ↩
Morand, S., Chaisiri, K., Kritiyakan, A., & Kumlert, R. (2020). Disease Ecology of Rickettsial Species: A Data Science Approach. Tropical Medicine and Infectious Disease, 5(2), 64. https://doi.org/10.3390/tropicalmed5020064 ↩
Yang D., Liu L. (2020) Solar Project Financing, Bankability, and Resource Assessment. In: Gandhi O., Srinivasan D. (eds) Sustainable Energy Solutions for Remote Areas in the Tropics. Green Energy and Technology. Springer, Cham https://link.springer.com/chapter/10.1007/978-3-030-41952-3_8 ↩
Hannon, B. A., Fairfield, W. D., Adams, B., Kyle, T., Crow, M., & Thomas, D. M. (2020). Use and abuse of dietary supplements in persons with diabetes. Nutrition & Diabetes, 10(1). https://doi.org/10.1038/s41387-020-0117-6 ↩
Neuts, B., van der Zee, E., Scheider, S., Nyamsuren, E., & Steenberghen, T. Topics and Sentiments in Online Place Reviews, an Innovative Way of Understanding the Perception of a City without Asking. https://conference.corp.at/archive/CORP2020_180.pdf ↩
Chandler, J. O., Haas, F. B., Khan, S., Bowden, L., Ignatz, M., Enfissi, E. M. A., … Leubner-Metzger, G. (2020). Rocket Science: The Effect of Spaceflight on Germination Physiology, Ageing, and Transcriptome of Eruca sativa Seeds. Life, 10(4), 49. https://doi.org/10.3390/life10040049 ↩
Greenhalgh, S. P., Rosenberg, J. M., Staudt Willet, K. B., Koehler, M. J., & Akcaoglu, M. (2020). Identifying multiple learning spaces within a single teacher-focused Twitter hashtag. Computers & Education, 148, 103809. https://doi.org/10.1016/j.compedu.2020.103809 ↩
Färber, L., van Gemert, R., Langangen, Ø., Durant, J. M., & Andersen, K. H. (2020). Population variability under stressors is dependent on body mass growth and asymptotic body size. Royal Society Open Science, 7(2), 192011. https://doi.org/10.1098/rsos.192011 ↩
Pyle, P., Foster, K. R., Godwin, C. M., Kaschube, D. R., & Saracco, J. F. (2020). Yearling proportion correlates with habitat structure in a boreal forest landbird community. PeerJ, 8, e8898. https://doi.org/10.7717/peerj.8898 ↩
Verhoeven, M. R., Glisson, W. J., & Larkin, D. J. (2020). Niche Models Differentiate Potential Impacts of Two Aquatic Invasive Plant Species on Native Macrophytes. Diversity, 12(4), 162. https://doi.org/10.3390/d12040162 ↩
Eastman, R. T., Roth, J. S., Brimacombe, K. R., Simeonov, A., Shen, M., Patnaik, S., & Hall, M. D. (2020). Remdesivir: A Review of Its Discovery and Development Leading to Emergency Use Authorization for Treatment of COVID-19. ACS Central Science, 6(5), 672–683. https://doi.org/10.1021/acscentsci.0c00489 ↩
Ozturk, R. C., & Altinok, I. (2020). Interaction of Plastics with Marine Species. Turkish Journal of Fisheries and Aquatic Sciences, 20(8). https://doi.org/10.4194/1303-2712-v20_8_07 ↩
DellaPosta, D., & Nee, V. (2020). Emergence of diverse and specialized knowledge in a metropolitan tech cluster. Social Science Research, 86, 102377. https://doi.org/10.1016/j.ssresearch.2019.102377 ↩
Ladwig, L. M., Zirbel, C. R., Sorenson, Q. M., & Damschen, E. I. (2020). A taxonomic, phylogenetic, and functional comparison of restoration seed mixes and historical plant communities in Midwestern oak savannas. Forest Ecology and Management, 466, 118122. https://doi.org/10.1016/j.foreco.2020.118122 ↩
Deza-Araujo, M., Morales-Molino, C., Tinner, W., Henne, P. D., Heitz, C., Pezzatti, G. B., … Conedera, M. (2020). A critical assessment of human-impact indices based on anthropogenic pollen indicators. Quaternary Science Reviews, 236, 106291. https://doi.org/10.1016/j.quascirev.2020.106291 ↩
Yang, D., & Bright, J. M. (2020). Worldwide validation of 8 satellite-derived and reanalysis solar radiation products: A preliminary evaluation and overall metrics for hourly data over 27 years. Solar Energy. https://doi.org/10.1016/j.solener.2020.04.016 ↩
Enkhbayar, A., Haustein, S., Barata, G., & Alperin, J. P. (2020). How much research shared on Facebook happens outside of public pages and groups? A comparison of public and private online activity around PLOS ONE papers. Quantitative Science Studies, 1–22. https://doi.org/10.1162/qss_a_00044 ↩
Van den Berg, S. J. P., Rendal, C., Focks, A., Butler, E., Peeters, E. T. H. M., De Laender, F., & Van den Brink, P. J. (2020). Potential impact of chemical stress on freshwater invertebrates: A sensitivity assessment on continental and national scale based on distribution patterns, biological traits, and relatedness. Science of The Total Environment, 731, 139150. https://doi.org/10.1016/j.scitotenv.2020.139150 ↩
Carroll, H. M., Wanamaker, A. D., Clark, L. G., & Wilsey, B. J. (2020). Ragweed and sagebrush pollen can distinguish between vegetation types at broad spatial scales. Ecosphere, 11(5). https://doi.org/10.1002/ecs2.3120 ↩
Kang, W., Zhang, M., Wang, Q., Gu, D., Huang, Z., Wang, H., … Jin, X. (2020). The SLC Family Are Candidate Diagnostic and Prognostic Biomarkers in Clear Cell Renal Cell Carcinoma. BioMed Research International, 2020, 1–17. https://doi.org/10.1155/2020/1932948 ↩
Feldmann, M. J., Hardigan, M. A., Famula, R. A., López, C. M., Tabb, A., Cole, G. S., & Knapp, S. J. (2020). Multi-dimensional machine learning approaches for fruit shape phenotyping in strawberry. GigaScience, 9(5). https://doi.org/10.1093/gigascience/giaa030 ↩
Marple, T. (2020). The social management of complex uncertainty: Central Bank similarity and crisis liquidity swaps at the Federal Reserve. The Review of International Organizations. https://doi.org/10.1007/s11558-020-09378-x ↩
Bubac, C. M., Miller, J. M., & Coltman, D. W. (2020). The genetic basis of animal behavioural diversity in natural populations. Molecular Ecology, 29(11), 1957–1971. https://doi.org/10.1111/mec.15461 ↩
Liu, Y., Wang, L., Lo, K.-W., & Lui, V. W. Y. (2020). Omics-wide quantitative B-cell infiltration analyses identify GPR18 for human cancer prognosis with superiority over CD20. Communications Biology, 3(1). https://doi.org/10.1038/s42003-020-0964-7 ↩
Callaghan, T., Karch, A., & Kroeger, M. (2020). Model State Legislation and Intergovernmental Tensions over the Affordable Care Act, Common Core, and the Second Amendment. Publius: The Journal of Federalism. https://doi.org/10.1093/publius/pjaa012 ↩
Rogers, A., O. Aburto-Oropeza, et al. 2020. Critical Habitats and Biodiversity: Inventory, Thresholds and Governance. Washington, DC: World Resources Institute. https://www.oceanpanel.org/blue-papers/critical-habitats-and-biodiversity-inventory-thresholds-and-governance ↩
Holzmeyer, L., Hartig, A.-K., Franke, K., Brandt, W., Muellner-Riehl, A. N., Wessjohann, L. A., & Schnitzler, J. (2020). Evaluation of plant sources for antiinfective lead compound discovery by correlating phylogenetic, spatial, and bioactivity data. Proceedings of the National Academy of Sciences, 117(22), 12444–12451. https://doi.org/10.1073/pnas.1915277117 ↩
Bramlett, B. H., & Burge, R. P. (2020). God Talk in a Digital Age: How Members of Congress Use Religious Language on Twitter. Politics and Religion, 1–23. https://doi.org/10.1017/s1755048320000231 ↩
Vogler, D., Udris, L., & Eisenegger, M. (2020). Measuring Media Content Concentration at a Large Scale Using Automated Text Comparisons. Journalism Studies, 1–20. https://doi.org/10.1080/1461670x.2020.1761865 ↩
CRAN: GitHub:
v0.1.0) of chirps is on CRAN - client for the Climate Hazards Group InfraRed Precipitation with Station Data. Checkout the docs to get started. chirps went through rOpenSci software review. v2.1.2) of skimr is on CRAN - compact and flexible summaries of data. See the release notes for changes. Checkout the vignettes to get started. v2.1.0/v2.1.1) of ijtiff are on CRAN - Comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started. v0.1.14) of spatsoc is on CRAN - detecting spatial and temporal groups in GPS relocations. See the release notes for changes. Checkout the docs to get started. v1.5.0) of fulltext is on CRAN - full text of scholarly articles across many data sources. See the release notes for changes. Checkout the fulltext book to get started. v1.1.0) of rcites is on CRAN - access the CITES Speciesplus database. See the release notes for changes. Checkout the docs to get started. v1.2/v1.3) of lightr are on CRAN - read spectrometric data and metadata. See the release notes for changes. Checkout the docs to get started. v7.12.4) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started. v0.4.0) of wikitaxa is on CRAN - taxonomic information from Wikipedia. See the release notes for changes. Checkout the docs to get started. v0.2.2) of pubchunks is on CRAN - Fetch Sections of XML Scholarly Articles. See the release notes for changes. Checkout the README to get started. v0.4.0) of crminer is on CRAN - Fetch scholarly full text from Crossref. See the release notes for changes. Checkout the README to get started. v0.7.7) of robotstxt is on CRAN - robots.txt parser and Webbot/Spider/Crawler permissions checker. See the release notes for changes. Checkout the docs to get started. v0.4.0) of sofa is on CRAN - Connector to CouchDB. See the release notes for changes. Checkout the vignettes to get started. v1.2.0/v1.2.1) of credentials are on CRAN - tools for managing ssh and git credentials. See the release notes for changes. Checkout the docs to get started. v1.0.0) of rdryad is on CRAN - R client for Dryad. See the release notes for changes. Checkout the README to get started. v0.3.4) of geojson is on CRAN - Classes for GeoJSON. See the release notes for changes. Checkout the vignettes to get started. v2.4.0) of magick is on CRAN - Advanced graphics and Image-Processing in R. See the release notes for changes. Checkout the vignette to get started. v3.0.0/v3.1.0) of rgbif are on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the occurrence manual to get started. v0.6.1) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. Software review is now accepting submissions again.
We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
No new submissions or approved submissions.
The following 25 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
A few new use cases were shared in the forum over the past two weeks since our last newsletter:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Check out our guidance for taking over maintenance of a package.
We’ve had nine recent examples of maintainer transitions within rOpenSci:
We’ve got one package in need of a new maintainer:
We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.
Rossi, M. (2020). Monitoring the vegetation dynamics and stress of mountainous grasslands using a multisensor approach. Dissertation. https://bit.ly/2Cf7BHF ↩
Jost, L., & Jansen, P. (2020). A novel approach to analyzing all trials in chronometric mental rotation and description of a flexible extended library of stimuli. OSF Preprints https://osf.io/y92fw ↩
Michaels, I. H., Pirani, S. J., & Carrascal, A. (2020). Visualizing 50 Years of Cancer Mortality Rates Across the US at Multiple Geographic Levels Using a Synchronized Map and Graph Animation. Preventing Chronic Disease, 17. https://doi.org/10.5888/pcd17.190286 ↩
Brick, C., McDowell, M., & Freeman, A. L. J. (2020). Risk communication in tables versus text: a registered report randomized trial on “fact boxes.” Royal Society Open Science, 7(3), 190876. https://doi.org/10.1098/rsos.190876 ↩
Yang, D. (2020). Choice of clear-sky model in solar forecasting. Journal of Renewable and Sustainable Energy, 12(2), 026101. https://doi.org/10.1063/5.0003495 ↩
Stropp, J., Umbelino, B., Correia, R. A., Campos-Silva, J. V., Ladle, R. J., & Malhado, A. C. M. (2020). The ghosts of forests past and future: deforestation and botanical sampling in the Brazilian Amazon. Ecography. https://doi.org/10.1111/ecog.05026 ↩
Claes, M., & Mäntylä, M. (2020). 20-MAD–20 Years of Issues and Commits of Mozilla and Apache Development. arXiv preprint arXiv:2003.14015. https://arxiv.org/pdf/2003.14015.pdf ↩
Trugman, A. T., Anderegg, L. D. L., Shaw, J. D., & Anderegg, W. R. L. (2020). Trait velocities reveal that mortality has driven widespread coordinated shifts in forest hydraulic trait composition. Proceedings of the National Academy of Sciences, 117(15), 8532–8538. https://doi.org/10.1073/pnas.1917521117 ↩
Zushi, Y., Hanari, N., Nabi, D., & Lin, B.-L. (2020). Mixture Touch: A Web Platform for the Evaluation of Complex Chemical Mixtures. ACS Omega, 5(14), 8121–8126. https://doi.org/10.1021/acsomega.0c00340 ↩
Martins, P. T., & Boeckx, C. (2020). Vocal learning: Beyond the continuum. PLOS Biology, 18(3), e3000672. https://doi.org/10.1371/journal.pbio.3000672 ↩
Hantgan-Sonko, A. (2020). Synchronic and diachronic strategies of mora preservation in Gújjolaay Eegimaa. Journal of African Languages and Literatures, (1), 1-25. http://www.politics.unina.it/index.php/jalalit/article/download/6732/7790 ↩
Fraser, N., Momeni, F., Mayr, P., & Peters, I. (2020). The relationship between bioRxiv preprints, citations and altmetrics. Quantitative Science Studies, 1–21. https://doi.org/10.1162/qss_a_00043 ↩
Staude, I. R., Waller, D. M., Bernhardt-Römermann, M., Bjorkman, A. D., Brunet, J., De Frenne, P., … Baeten, L. (2020). Replacements of small- by large-ranged species scale up to diversity loss in Europe’s temperate forest biome. Nature Ecology & Evolution, 4(6), 802–808. https://doi.org/10.1038/s41559-020-1176-8 ↩
Hernández‐Rojas, A. C., Kluge, J., Krömer, T., Carvajal‐Hernández, C., Silva‐Mijangos, L., Miehe, G., … Kessler, M. (2020). Latitudinal patterns of species richness and range size of ferns along elevational gradients at the transition from tropics to subtropics. Journal of Biogeography, 47(6), 1383–1397. https://doi.org/10.1111/jbi.13841 ↩
Cui, X., Paterson, A. M., Wyse, S. V., Alam, M. A., Maurin, K. J. L., Pieper, R., … Curran, T. J. (2020). Shoot flammability of vascular plants is phylogenetically conserved and related to habitat fire-proneness and growth form. Nature Plants, 6(4), 355–359. https://doi.org/10.1038/s41477-020-0635-1 ↩
Timpano, E. K., Scheible, M. K. R., & Meiklejohn, K. A. (2020). Optimization of the second internal transcribed spacer (ITS2) for characterizing land plants from soil. PLOS ONE, 15(4), e0231436. https://doi.org/10.1371/journal.pone.0231436 ↩
Bärenstrauch, M., Mann, S., Jacquemin, C., Bibi, S., Sylla, O.-K., Baudouin, E., … Kunz, C. (2020). Molecular crosstalk between the endophyte Paraconiothyrium variabile and the phytopathogen Fusarium oxysporum – Modulation of lipoxygenase activity and beauvericin production during the interaction. Fungal Genetics and Biology, 139, 103383. https://doi.org/10.1016/j.fgb.2020.103383 ↩
Zhao, P., & Cao, Y. (2020). Commuting inequity and its determinants in Shanghai: New findings from big-data analytics. Transport Policy, 92, 20–37. https://doi.org/10.1016/j.tranpol.2020.03.006 ↩
Mishler, B. D., Guralnick, R., Soltis, P. S., Smith, S. A., Soltis, D. E., Barve, N., … Laffan, S. W. (2020). Spatial phylogenetics of the North American flora. Journal of Systematics and Evolution. https://doi.org/10.1111/jse.12590 ↩
Sinval, J., & Marôco, J. (2020). Short Index of Job Satisfaction: Validity evidence from Portugal and Brazil. PLOS ONE, 15(4), e0231474. https://doi.org/10.1371/journal.pone.0231474 ↩
Barela, I., Burger, L. M., Taylor, J., Evans, K. O., Ogawa, R., McClintic, L., & Wang, G. (2020). Relationships between survival and habitat suitability of semi‐aquatic mammals. Ecology and Evolution, 10(11), 4867–4875. https://doi.org/10.1002/ece3.6239 ↩
Menounos, B., Pelto, B. M., Fleming, S. W., Moore, R. D., Weber, F., Hutchinson, D., & Brahney, J. (2020). Glaciers in the Canadian Columbia Basin, Technical Report. https://digitalcommons.usu.edu/cgi/viewcontent.cgi?article=2134&context=wats_facpub ↩
Bernardi, A. P., Lauterjung, M. B., Mantovani, A., & dos Reis, M. S. (2020). Phylogeography and species distribution modeling reveal a historic disjunction for the conifer Podocarpus lambertii. Tree Genetics & Genomes, 16(3). https://doi.org/10.1007/s11295-020-01434-2 ↩
Martínez, A., Eckert, E. M., Artois, T., Careddu, G., Casu, M., Curini-Galletti, M., … Fontaneto, D. (2020). Human access impacts biodiversity of microscopic animals in sandy beaches. Communications Biology, 3(1). https://doi.org/10.1038/s42003-020-0912-6 ↩
Hagan, A. K., Pollet, R. M., & Libertucci, J. (2020). Suggestions for Improving Invited Speaker Diversity To Reflect Trainee Diversity. Journal of Microbiology & Biology Education, 21(1). https://doi.org/10.1128/jmbe.v21i1.2105 ↩
CRAN: GitHub:
v2.4.5) of RNeXML is on CRAN - Semantically Rich I/O for the NeXML Format. See the release notes for changes. Checkout the docs to get started. v1.1.0) of bold is on CRAN - interface to Bold Systems (http://www.boldsystems.org/) API. See the release notes for changes. Checkout the docs to get started. v0.1.3) of outsider.base is on CRAN - base package for outsider. See the release notes for changes. Checkout the docs to get started. v2.1.1) of GSODR is on CRAN - Global Surface Summary of the Day (GSOD) Weather Data from R. See the release notes for changes. Checkout the docs to get started. v1.0.0) of rnoaa is on CRAN - NOAA Weather Data from R. See the release notes for changes. Checkout the docs to get started. v0.6.0) of brranching is on CRAN - Fetch Phylogenies from Many Sources. See the release notes for changes. Checkout the docs to get started. v0.4.0) of originr is on CRAN - Fetch species origin data from the web. See the release notes for changes. Checkout the docs to get started. v0.2.3.0) of opentripplanner is on CRAN - client for OpenTripPlanner for journey planning. See the release notes for changes. Checkout the docs to get started. v0.9.97) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started. v1.1.2) of dbparser is on CRAN - DrugBank database XML parser. See the release notes for changes. Checkout the docs to get started. v1.0.0) of rbison is on CRAN - interface to the USGS BISON API. See the release notes for changes. Checkout the docs to get started. Software review is now accepting submissions again.
We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following package was recently submitted:
It’s time for another installment of … 2 Months in 2 Minutes - rOpenSci News, June 2020 - if you want a brief summary of the last 2 months of these newsletters, these blog posts are for you (written by Stefanie Butland)
The following 27 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
Many new use cases were shared in the forum over the past month since our last newsletter:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Check out our guidance for taking over maintenance of a package.
We’ve had nine recent examples of maintainer transitions within rOpenSci:
We’ve got one package in need of a new maintainer:
We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.
Wesener, F., Szymczak, A., Rillig, M. C., & Tietjen, B. (2020). Stress priming affects fungal competition – evidence from a combined experimental and modeling study. https://doi.org/10.1101/2020.03.04.976357 ↩
Deribe, K., Simpson, H., Pullan, R. L., Bosco, M. J., Wanji, S., Weaver, N. D., … Cano, J. (2020). Predicting the Environmental Suitability and Population at Risk of Podoconiosis in Africa. https://doi.org/10.1101/2020.03.04.977827 ↩
Parravicini, V., Casey, J. M., Schiettekatte, N. M. D., Brandl, S. J., Pozas-Schacre, C., Carlot, J., … Vii, J. (2020). Global gut content data synthesis and phylogeny delineate reef fish trophic guilds. https://doi.org/10.1101/2020.03.04.977116 ↩
Vantas, K., Sidiropoulos, E., & Loukas, A. (2020). Estimating Current and Future Rainfall Erosivity in Greece Using Regional Climate Models and Spatial Quantile Regression Forests. Water, 12(3), 687. https://doi.org/10.3390/w12030687 ↩
Ashby, M. P. J. (2020, March 6). Three quarters of new criminological knowledge is hidden from policy makers. https://doi.org/10.31235/osf.io/wnq7h ↩
Yu, G. (2020). Using ggtree to Visualize Data on Tree‐Like Structures. Current Protocols in Bioinformatics, 69(1). https://doi.org/10.1002/cpbi.96 ↩
Lequime, S., Bastide, P., Dellicour, S., Lemey, P., & Baele, G. (2020). nosoi: a stochastic agent-based transmission chain simulation framework in R. https://doi.org/10.1101/2020.03.03.973107 ↩
Wei, N., Kaczorowski, R. L., Arceo-Gómez, G., O’Neill, E. M., Hayes, R. A., & Ashman, T.-L. (2020). Pollinator niche partitioning and asymmetric facilitation contribute to the maintenance of diversity. https://doi.org/10.1101/2020.03.02.974022 ↩
Fontanelli, O., & Mansilla, R. (2020). Modeling the Popularity of Twitter Hashtags with Master Equations. arXiv preprint, https://arxiv.org/pdf/2003.02672.pdf ↩
Young, N. E., Jarnevich, C. S., Sofaer, H. R., Pearse, I., Sullivan, J., Engelstad, P., & Stohlgren, T. J. (2020). A modeling workflow that balances automation and human intervention to inform invasive plant management decisions at multiple spatial scales. PLOS ONE, 15(3), e0229253. https://doi.org/10.1371/journal.pone.0229253 ↩
Allen, D., & Kim, A. Y. (2020). A permutation test and spatial cross-validation approach to assess models of interspecific competition between trees. PLOS ONE, 15(3), e0229930. https://doi.org/10.1371/journal.pone.0229930 ↩
Borgoni, R., Gilardi, A., & Zappa, D. (2020). Assessing the Risk of Car Crashes in Road Networks. Social Indicators Research. https://doi.org/10.1007/s11205-020-02295-x ↩
Dadi, B. B. (2020). Modeling malaria cases associated with environmental risk factors in Ethiopia using geographically weighted regression (Doctoral dissertation). http://repositori.uji.es/xmlui/bitstream/handle/10234/187004/TFM_Berhanu.pdf?sequence=1&isAllowed=y ↩
Pruchnik, P. (2020). Identification of Trends in the Polish Media on the Example of the Quarterly Studia Medioznawcze The Use of Big Data Tools. Media Studies, 80(1). http://yadda.icm.edu.pl/yadda/element/bwmeta1.element.desklight-e79ed2c7-fd7d-4a91-8895-c322743c8f48/c/04_Pruchnik_EN.pdf ↩
Pavlovich, S. S., Darling, T., Hume, A. J., Davey, R. A., Feng, F., Mühlberger, E., & Kepler, T. B. (2020). Egyptian Rousette IFN-ω Subtypes Elicit Distinct Antiviral Effects and Transcriptional Responses in Conspecific Cells. Frontiers in Immunology, 11. https://doi.org/10.3389/fimmu.2020.00435 ↩
Hagen, L., Neely, S., Keller, T. E., Scharf, R., & Vasquez, F. E. (2020). Rise of the Machines? Examining the Influence of Social Bots on a Political Discussion Network. Social Science Computer Review, 089443932090819. https://doi.org/10.1177/0894439320908190 ↩
Chakraborty, T. (2020). Multi-scale assessment of drought-induced forest dieback (Doctoral dissertation). https://run.unl.pt/bitstream/10362/94403/1/TGEO0243.pdf ↩
Salgado, D., & Oancea, B. (2020). On new data sources for the production of official statistics. arXiv preprint https://arxiv.org/pdf/2003.06797.pdf ↩
Jézéquel, C., Tedesco, P. A., Bigorne, R., Maldonado-Ocampo, J. A., Ortega, H., Hidalgo, M., … Oberdorff, T. (2020). A database of freshwater fish species of the Amazon Basin. Scientific Data, 7(1). https://doi.org/10.1038/s41597-020-0436-4 ↩
Chapman, A., Belbin, L., Zermoglio, P., Wieczorek, J., Morris, P., Nicholls, M., … Schigel, D. (2020). Developing Standards for Improved Data Quality and for Selecting Fit for Use Biodiversity Data. Biodiversity Information Science and Standards, 4. https://doi.org/10.3897/biss.4.50889 ↩
Hamilton, L. M., & Lahne, J. (2020). Fast and automated sensory analysis: Using natural language processing for descriptive lexicon development. Food Quality and Preference, 83, 103926. https://doi.org/10.1016/j.foodqual.2020.103926 ↩
Ranghetti, L., Boschetti, M., Nutini, F., & Busetto, L. (2020). “sen2r”: An R toolbox for automatically downloading and preprocessing Sentinel-2 satellite data. Computers & Geosciences, 139, 104473. https://doi.org/10.1016/j.cageo.2020.104473 ↩
Moran, N. P., Sánchez-Tójar, A., Schielzeth, H., & Reinhold, K. (2020). Poor condition promotes high-risk behaviours but context-dependency is key: A systematic review and meta-analysis. Ecorxiv preprint. https://ecoevorxiv.org/xsehd/ ↩
Lindner, M., Gilhooley, M. J., Palumaa, T., Morton, A. J., Hughes, S., & Hankins, M. W. (2020). Expression and Localization of Kcne2 in the Vertebrate Retina. Investigative Opthalmology & Visual Science, 61(3), 33. https://doi.org/10.1167/iovs.61.3.33 ↩
Wang, Y., Zhang, X., Song, Q., Hou, Y., Liu, J., Sun, Y., & Wang, P. (2020). Characterization of the chromatin accessibility in an Alzheimer’s disease (AD) mouse model. Alzheimer’s Research & Therapy, 12(1). https://doi.org/10.1186/s13195-020-00598-2 ↩
Hoffman, M. M., Zylla, J. S., Bhattacharya, S., Calar, K., Hartman, T. W., Bhardwaj, R. D., … Messerli, S. M. (2020). Analysis of Dual Class I Histone Deacetylase and Lysine Demethylase Inhibitor Domatinostat (4SC-202) on Growth and Cellular and Genomic Landscape of Atypical Teratoid/Rhabdoid. Cancers, 12(3), 756. https://doi.org/10.3390/cancers12030756 ↩
Bastide, P., Ho, L. S. T., Baele, G., Lemey, P., & Suchard, M. A. (2020). Efficient Bayesian Inference of General Gaussian Models on Large Phylogenetic Trees. arXiv preprint arXiv:2003.10336. https://arxiv.org/pdf/2003.10336 ↩
CRAN: GitHub:
v1.1.2) of dbparser is on CRAN - DrugBank database XML parser. See the release notes for changes. Checkout the docs to get started. v1.0.4) of fingertipsR is on CRAN - Fingertips data for public health http://fingertips.phe.org.uk/. See the release notes for changes. Checkout the docs to get started. v0.3.9) of jstor is on CRAN - read data from JSTOR/DfR. See the release notes for changes. Checkout the docs to get started. v7.12.2) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started. v1.3.8) of skynet is on CRAN - Bureau of Transport Statistics Data client. See the release notes for changes. Checkout the docs to get started. v0.4) of europepmc is on CRAN - Interface to the Europe PubMed Central RESTful web service. See the release notes for changes. Checkout the docs to get started. v0.7.4) of robotstxt is on CRAN - robots.txt parser and Webbot/Spider/Crawler permissions checker. See the release notes for changes. Checkout the docs to get started. v2.3) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the occurrence manual to get started. v1.0.0) of webchem is on CRAN - Chemical information from the web. See the release notes for changes. Checkout the docs to get started. v2.2) of jsonld is on CRAN - JSON for linking data. See the release notes for changes. Checkout the README to get started. v0.9.1) of hddtools is on CRAN - Hydrological Data Discovery Tools. See the release notes for changes. Checkout the docs to get started. v2.3.1) of pdftools is on CRAN - Text extraction, rendering and converting of PDF documents. See the release notes for changes. Checkout the README to get started. v3.1.3) of qualtRics is on CRAN - download Qualtrics survey data. See the release notes for changes. Checkout the docs to get started. v0.9.96) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started. v0.3.0) of geoops is on CRAN - GeoJSON topology calculations and operations. See the release notes for changes. Checkout the docs to get started. v1.4.2) of xslt is on CRAN - extensible style-sheet language transformations. See the release notes for changes. Checkout the README to get started. v1.0.0) of natserv is on CRAN - NatureServe R Interface. See the release notes for changes. Checkout the docs to get started. v0.1.5) of textreuse is on CRAN - detect text reuse and document similarity. See the release notes for changes. Checkout the docs to get started. v0.2.4) of tidync is on CRAN - a tidy approach to NetCDF data exploration and extraction. See the release notes for changes. Checkout the docs to get started. v2.0-15) of CoordinateCleaner is on CRAN - automated cleaning of occurrence records from biological collections. See the release notes for changes. Checkout the docs to get started. Software review is now accepting submissions again.
We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following two packages were recently submitted:
Jeroen Ooms wrote about a new version of the rsvg package: Superior svg graphics rendering in R, and why it matters.
The following 26 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
Many new use cases were shared in the forum over the past month since our last newsletter:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had nine recent examples of maintainer transitions within rOpenSci:
We’ve got one package in need of a new maintainer:
We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.
Perez‐Lamarque, B., Selosse, M., Öpik, M., Morlon, H., & Martos, F. (2020). Cheating in arbuscular mycorrhizal mutualism: a network and phylogenetic analysis of mycoheterotrophy. New Phytologist. https://doi.org/10.1111/nph.16474 ↩
Larson, J. E., Anacker, B. L., Wanous, S., & Funk, J. L. (2020). Ecological strategies begin at germination: Traits, plasticity and survival in the first 4 days of plant life. Functional Ecology. https://doi.org/10.1111/1365-2435.13543 ↩
Rodrigues, B. N., & Boscolo, D. (2020). Do bipartite binary antagonistic and mutualistic networks have different responses to the taxonomic resolution of nodes? Ecological Entomology. https://doi.org/10.1111/een.12844 ↩
Manel, S., Guerin, P.-E., Mouillot, D., Blanchet, S., Velez, L., Albouy, C., & Pellissier, L. (2020). Global determinants of freshwater and marine fish genetic diversity. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-14409-7 ↩
Thompson, K. A. (2020). Experimental hybridization studies suggest that pleiotropic alleles commonly underlie adaptive divergence between natural populations. The American Naturalist. https://doi.org/10.1086/708722 ↩
Gent, D. H., Claassen, B. J., Gadoury, D. M., Grünwald, N. J., Knaus, B. J., Radišek, S., … Wolfenbarger, S. N. (2020). Population Diversity and Structure of Podosphaera macularis in the Pacific Northwestern United States and Other Populations. Phytopathology, PHYTO–12–19–044. https://doi.org/10.1094/phyto-12-19-0448-r ↩
Bagheri, H. 2019. Domain-specific language and infrastructure for genomics. Graduate Theses and Dissertations. 17641. https://lib.dr.iastate.edu/etd/17641 ↩
Heisel, S. E. (2019). Ecological, Genomic, and Social Factors Impacting Wildlife Conservation (Doctoral dissertation, University of Georgia). https://search.proquest.com/docview/2357432037 ↩
Hannah, L., Roehrdanz, P. R., Marquet, P. A., Enquist, B. J., Midgley, G., Foden, W., … Svenning, J. (2020). 30% land conservation and climate action reduces tropical extinction risk by more than 50%. Ecography. https://doi.org/10.1111/ecog.05166 ↩
Ryt-Hansen, P., Pedersen, A. G., Larsen, I., Kristensen, C. S., Krog, J. S., Wacheck, S., & Larsen, L. E. (2020). Substantial Antigenic Drift in the Hemagglutinin Protein of Swine Influenza A Viruses. Viruses, 12(2), 248. https://doi.org/10.3390/v12020248 ↩
Armitage, D. W., & Jones, S. E. (2020). Barriers to coexistence limit the poleward range of a globally-distributed plant. https://doi.org/10.1101/2020.02.24.946574 ↩
Hamid M., Khuroo A.A., Ahmad R., Rasheed S., Malik A.H., Dar G.H. (2020) Threatened Flora of Jammu and Kashmir State. In:Dar G., Khuroo A. (eds) Biodiversity of the Himalaya:Jammu and Kashmir State. Topics in Biodiversity and Conservation, vol 18. Springer, Singapore https://doi.org/10.1007/978-981-32-9174-4_37 ↩
Kaczvinsky, C., & Hardy, N. B. (2020). Do major host shifts spark diversification in butterflies? Ecology and Evolution, 10(8), 3636–3646. https://doi.org/10.1002/ece3.6116 ↩
Zizka, A., Carvalho‐Sobrinho, J. G., Pennington, R. T., Queiroz, L. P., Alcantara, S., Baum, D. A., … Antonelli, A. (2020). Transitions between biomes are common and directional in Bombacoideae (Malvaceae). Journal of Biogeography. https://doi.org/10.1111/jbi.13815 ↩
Jung, E.-Y., Gaviria, J., Sun, S., & Engelbrecht, B. M. J. (2020). Comparative drought resistance of temperate grassland species: testing performance trade-offs and the relation to distribution. Oecologia, 192(4), 1023–1036. https://doi.org/10.1007/s00442-020-04625-9 ↩
Howard, C. C., & Cellinese, N. (2020). Tunicate bulb size variation in monocots explained by temperature and phenology. Ecology and Evolution, 10(5), 2299–2309. https://doi.org/10.1002/ece3.5996 ↩
Du, C., Chen, J., Jiang, L., & Qiao, G. (2020). High correlation of species diversity patterns between specialist herbivorous insects and their specific hosts. Journal of Biogeography. https://doi.org/10.1111/jbi.13816 ↩
Long, J. D., & Turner, D. (2020). Applied R in the Classroom. Australian Economic Review, 53(1), 139–157. https://doi.org/10.1111/1467-8462.12362 ↩
Reyes, J. A., & Lira-Noriega, A. (2020). Current and future global potential distribution of the fruit fly Drosophila suzukii (Diptera: Drosophilidae). The Canadian Entomologist, 1–13. https://doi.org/10.4039/tce.2020.3 ↩
Lara-Lizardi, F., Hoyos-Padilla, M., Hearn, A., Klimley, A. P., Galván-Magaña, F., Arauz, R., … Ketchum, J. T. (2020). Shark movements in the Revillagigedo Archipelago and connectivity with the Eastern Tropical Pacific. https://doi.org/10.1101/2020.03.02.972844 ↩
Cichosz, P. (2020). Unsupervised modeling anomaly detection in discussion forums posts using global vectors for text representation. Natural Language Engineering, 1–28. https://doi.org/10.1017/s1351324920000066 ↩
Pietzke, M., Vazquez, A. 2020. Metabolite AutoPlotter–an application to automatically process and visualise metabolite data in the web-browser. https://assets.researchsquare.com/files/6b8d169e-e621-4ebd-8c6e-ff607a788ebe/v1/Manuscript.pdf ↩
Kusumoto, B., Costello, M. J., Kubota, Y., Shiono, T., Wei, C., Yasuhara, M., & Chao, A. (2020). Global distribution of coral diversity: Biodiversity knowledge gradients related to spatial resolution. Ecological Research, 35(2), 315–326. https://doi.org/10.1111/1440-1703.12096 ↩
Potter, R. J. (2019). Machine learning for resource economics; a review of modern computational statistics with empirical applications in fisheries management (Master’s thesis). https://openaccess.nhh.no/nhh-xmlui/bitstream/handle/11250/2644607/masterthesis.pdf?sequence=1 ↩
Marshall, D. J., Pettersen, A. K., Bode, M., & White, C. R. (2020). Developmental cost theory predicts thermal environment and vulnerability to global warming. Nature Ecology & Evolution, 4(3), 406–411. https://doi.org/10.1038/s41559-020-1114-9 ↩
Amiri Roudbar, M., Mohammadabadi, M. R., Ayatollahi Mehrgardi, A., Abdollahi-Arpanahi, R., Momen, M., Morota, G., … Rosa, G. J. M. (2020). Integration of single nucleotide variants and whole-genome DNA methylation profiles for classification of rheumatoid arthritis cases from controls. Heredity, 124(5), 658–674. https://doi.org/10.1038/s41437-020-0301-4 ↩
CRAN: GitHub:
v1.1.1) of dbparser is on CRAN - DrugBank database XML parser. See the release notes for changes. Checkout the docs to get started. v1.4.0) of MODIStsp is on CRAN - Automate Download and Preprocessing of MODIS Land Products Data. See the release notes for changes. Checkout the docs to get started. v2.4.4) of RNeXML is on CRAN - Semantically Rich I/O for the NeXML Format. See the release notes for changes. Checkout the docs to get started. v0.1.1) of colocr is on CRAN - conduct co-localization analysis of fluorescence microscopy images. See the release notes for changes. Checkout the docs to get started. v0.3.2) of cRegulome is on CRAN - access, manage and visualize regulome (microRNA/transcription factors)-gene correlations in cancer. See the release notes for changes. Checkout the docs to get started. v0.3.6) of eia is on CRAN - API wrapper for US Energy Information Administration open data. See the release notes for changes. Checkout the docs to get started. v2.3.6) of beautier is on CRAN - create BEAST2 input files programmatically. See the release notes for changes. Checkout the docs to get started. v2.1) of tracerer is on CRAN - parse and analyze BEAST2 input files programmatically. See the release notes for changes. Checkout the docs to get started. v1.3) of writexl is on CRAN - a portable, light-weight data frame to xlsx exporter. See the release notes for changes. Checkout the README to get started. v0.27.1) of git2r is on CRAN - an interface to the libgit2 library, a pure C implementation of the Git core methods. See the release notes for changes. Checkout the README to get started. v0.6.0) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. v1.0.0) of bold is on CRAN - interface to Bold Systems (http://www.boldsystems.org/) API. See the release notes for changes. Checkout the docs to get started. v0.3.4) of taxa is on CRAN - taxonomic classes for groupings of taxonomic names without data, and those with data. See the release notes for changes. Checkout the docs to get started. v0.9.95) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started. In the interest of reducing load on reviewers and editors as we manage the COVID-19 crisis, rOpenSci is temporarily pausing new submissions for software peer review. Please check back at our software review repository for updates. In this period new submissions will not be handled, nor new reviewers assigned. Reviews and responses to reviews will be handled on a ‘best effort’ basis, but no follow-up reminders will be sent. Other rOpenSci community activities continue. We express our continued great appreciation for the work of our authors and reviewers.
Maëlle Salmon has two blog posts in the past two weeks:
The following 23 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
A few new use cases were shared in the forum recently:
testing: Why You Should Document Your Tests Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had eight recent examples of maintainer transitions within rOpenSci:
We’ve got one package in need of a new maintainer:
We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.
Adil, S. H., Ebrahim, M., Ali, S. S. A., & Raza, K. 2019. Identifying Trends in Data Science Articles using Text Mining. In 2019 4th International Conference on Emerging Trends in Engineering, Sciences and Technology (ICEEST) (pp. 1-7). IEEE. https://ieeexplore.ieee.org/document/8981702 ↩
Finoshin, A. D., Adameyko, K. I., Mikhailov, K. V., Kravchuk, O. I., Georgiev, A. A., Gornostaev, N. G., … Lyupina, Y. V. (2020). Iron metabolic pathways in the processes of sponge plasticity. PLOS ONE, 15(2), e0228722. https://doi.org/10.1371/journal.pone.0228722 ↩
Pimiento, C., & Benton, M. J. (2020). The impact of the Pull of the Recent on extant elasmobranchs. Palaeontology. https://doi.org/10.1111/pala.12478 ↩
Benhadi‐Marín, J., Santos, S. A. P., Baptista, P., & Pereira, J. A. (2020). Distribution of Bactrocera oleae (Rossi, 1790) throughout the Iberian Peninsula based on a maximum entropy modeling approach. Annals of Applied Biology. https://doi.org/10.1111/aab.12584 ↩
Ahrenfeldt, J., Waisi, M., Loft, I. C., Clausen, P. T. L. C., Allesøe, R., Szarvas, J., … Lund, O. (2020). Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-59292-w ↩
Cinelli, M. (2019). Generalized rich-club ordering in networks. Journal of Complex Networks, 7(5), 702–719. https://doi.org/10.1093/comnet/cnz002 ↩
Alfaro-Ramírez, F. U., Ramírez-Albores, J. E., Vargas-Hernández, J. J., Franco-Maass, S., & Pérez-Suárez, M. (2020). Potential reduction of Hartweg´s Pine (Pinus hartwegii Lindl.) geographic distribution. PLOS ONE, 15(2), e0229178. https://doi.org/10.1371/journal.pone.0229178 ↩
Martinez-Feria, R. A., & Basso, B. (2020). Unstable crop yields reveal opportunities for site-specific adaptations to climate variability. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-59494-2 ↩
Rego, A., Sousa, A. G. G., Santos, J. P., Pascoal, F., Canário, J., Leão, P. N., & Magalhães, C. (2020). Diversity of Bacterial Biosynthetic Genes in Maritime Antarctica. Microorganisms, 8(2), 279. https://doi.org/10.3390/microorganisms8020279 ↩
Cederwall, J., Black, T. A., Blais, J. M., Hanson, M. L., Hollebone, B. P., Palace, V. P., … Orihel, D. M. (2020). Life under an oil slick: response of a freshwater food web to simulated spills of diluted bitumen in field mesocosms. Canadian Journal of Fisheries and Aquatic Sciences, 77(5), 779–788. https://doi.org/10.1139/cjfas-2019-0224 ↩
Mossion, V., Dauphin, B., Grant, J., Zemp, N., & Croll, D. (2020). A reference transcriptome for the early-branching fern Botrychium lunaria enables fine-grained resolution of population structure. https://doi.org/10.1101/2020.02.17.952283 ↩
Funk, B., Sadeh-Sharvit, S., Fitzsimmons-Craft, E. E., Trockel, M. T., Monterubio, G. E., Goel, N. J., … Taylor, C. B. (2020). A Framework for Applying Natural Language Processing in Digital Health Interventions. Journal of Medical Internet Research, 22(2), e13855. https://doi.org/10.2196/13855 ↩
Correia, C. N., McLoughlin, K. E., Nalpas, N. C., Magee, D. A., Browne, J. A., Rue-Albrecht, K., … MacHugh, D. E. (2018). RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses (Equus caballus) and Cattle (Bos taurus). Frontiers in Genetics, 9. https://doi.org/10.3389/fgene.2018.00278 ↩
Verde Arregoitia, L. D., Teta, P., & D’Elía, G. (2020). Patterns in research and data sharing for the study of form and function in caviomorph rodents. Journal of Mammalogy. https://doi.org/10.1093/jmammal/gyaa002 ↩
Shivambu, T. C., Shivambu, N., & Downs, C. T. (2020). Impact assessment of seven alien invasive bird species already introduced to South Africa. Biological Invasions. https://doi.org/10.1007/s10530-020-02221-9 ↩
Jhwueng, D.-C., & O’Meara, B. C. (2020). On the Matrix Condition of Phylogenetic Tree. Evolutionary Bioinformatics, 16, 117693432090172. https://doi.org/10.1177/1176934320901721 ↩
Cooke, R. S. C., Eigenbrod, F., & Bates, A. E. (2020). Ecological distinctiveness of birds and mammals at the global scale. Global Ecology and Conservation, 22, e00970. https://doi.org/10.1016/j.gecco.2020.e00970 ↩
Palanisamy, S. (2019). An analysis on hidden markov model prediction factors using California wildfire and meteorological records (Doctoral dissertation, California State University, Sacramento). https://bit.ly/2yCWk2M ↩
Panayiotou, C. (2020). An Ontological Analysis and Natural Language Processing of Figures of Speech. International Journal of Artificial Intelligence & Applications, 11(1), 17–30. https://doi.org/10.5121/ijaia.2020.11102 ↩
Ji, Y., Baker, C. C., Li, Y., Popescu, V. D., Wang, Z., Wang, J., … Yu, D. W. (2020). Large-scale Quantification of Vertebrate Biodiversity in Ailaoshan Nature Reserve from Leech iDNA. https://doi.org/10.1101/2020.02.10.941336 ↩
Li, X., & Guo, B. (2020). Substantially adaptive potential in polyploid cyprinid fishes: evidence from biogeographic, phylogenetic and genomic studies. Proceedings of the Royal Society B: Biological Sciences, 287(1920), 20193008. https://doi.org/10.1098/rspb.2019.3008 ↩
Silva, I., Crane, M., Marshall, B. M., & Strine, C. T. (2020). Revisiting reptile home ranges: moving beyond traditional estimators with dynamic Brownian Bridge Movement Models. https://doi.org/10.1101/2020.02.10.941278 ↩
Schwalb‐Willmann, J., Remelgado, R., Safi, K., & Wegmann, M. (2020). moveVis: Animating movement trajectories in synchronicity with static or temporally dynamic environmental data in R. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13374 ↩
CRAN: GitHub:
v1.1.3) of lingtypology is on CRAN - linguistic typology and mapping. See the release notes for changes. Checkout the docs to get started. v1.24.1) of rtika is on CRAN - R Interface to Apache Tika. See the release notes for changes. Checkout the docs to get started. v0.3.0) of googleLanguageR is on CRAN - Google’s Natural Language, Cloud Translation, Cloud Speech, and Cloud Text-to-Speech APIs. See the release notes for changes. Checkout the docs to get started. v2.1.0) of GSODR is on CRAN - Global Surface Summary of the Day (GSOD) Weather Data from R. See the release notes for changes. Checkout the docs to get started. v0.4.0) of natserv is on CRAN - NatureServe R Interface. See the release notes for changes. Checkout the docs to get started. v0.9.0) of ritis is on CRAN - an R client for ITIS (Integrated Taxonomic Information Service). See the release notes for changes. Checkout the docs to get started. v0.3.4) of weathercan is on CRAN - Download weather data from the Environment and Climate Change Canada website. See the release notes for changes. Checkout the docs to get started. v0.3.0) of citecorp is on CRAN - client for the Open Citations Corpus. See the release notes for changes. Checkout the docs to get started. v1.0.3) of fingertipsR is on CRAN - Fingertips data for public health http://fingertips.phe.org.uk/. See the release notes for changes. Checkout the vignettes to get started. v2.1.1) of skimr is on CRAN - compact and flexible summaries of data. See the release notes for changes. Checkout the vignettes to get started. v1.4.1) of xslt is on CRAN - extensible style-sheet language transformations. See the release notes for changes. Checkout the README to get started. v0.2.1.0) of opentripplanner is on CRAN - client for OpenTripPlanner for journey planning. See the release notes for changes. Checkout the docs to get started. v0.5.0) of fauxpas is on CRAN - HTTP error classes. See the release notes for changes. Checkout the vignette to get started. In the interest of reducing load on reviewers and editors as we manage the COVID-19 crisis, rOpenSci is temporarily pausing new submissions for software peer review. Please check back at our software review repository after 17 April for updates. In this period new submissions will not be handled, nor new reviewers assigned. Reviews and responses to reviews will be handled on a ‘best effort’ basis, but no follow-up reminders will be sent. Other rOpenSci community activities continue. We express our continued great appreciation for the work of our authors and reviewers.
There’s a new version of the rOpenSci Dev Guide. The software review editors wrote a post describing the accumulated changes since v0.3: rOpenSci Dev Guide 0.4.0: Updates. Some highlights:
It’s time for another installment of … 2 Months in 2 Minutes - rOpenSci News, April 2020 - if you want a brief summary of the last 2 months of these newsletters, these blog posts are for you (written by Stefanie Butland)
Matthew Lau wrote a post on their package (Rclean) that recently went through rOpenSci software review: Automatic Code Cleaning in R with Rclean
Matthew Strimas-Mackey wrote a blog post on Extracting eBird Data from a Polygon using the auk package.
Maëlle Salmon has a nice blog post about R Markdown and Hugo learnings! Miscellaneous Wisdom about R Markdown & Hugo Gained from Work on our Website
The following 20 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
A few new use cases were shared in the forum recently:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had eight recent examples of maintainer transitions within rOpenSci:
We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.
We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.
Benito, B. M., & Birks, H. J. B. (2020). distantia: an open‐source toolset to quantify dissimilarity between multivariate ecological time‐series. Ecography. https://doi.org/10.1111/ecog.04895 ↩
Ceschin, D. G., Pires, N. S., Mardirosian, M. N., Lascano, C. I., & Venturino, A. (2020). The Rhinella arenarum transcriptome: de novo assembly, annotation and gene prediction. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-57961-4 ↩
von Schmidt, A., Cyganski, R., & Heinrichs, M. 2019. Web-based Visualization of Daily Mobility Patterns in R. International Journal on Advances in Internet Technology, vol 12 (3 & 4). https://elib.dlr.de/133599/1/inttech_v12_n34_2019_2.pdf ↩
Oliphant, K., Cochrane, K., Schroeter, K., Daigneault, M. C., Yen, S., Verdu, E. F., & Allen-Vercoe, E. (2020). Effects of Antibiotic Pretreatment of an Ulcerative Colitis-Derived Fecal Microbial Community on the Integration of Therapeutic Bacteria In Vitro. mSystems, 5(1). https://doi.org/10.1128/msystems.00404-19 ↩
Lourenço, A. F. P. (2019). Eco-evolutionary implications underlying the emergence of a derived reproductive mode in fire salamanders. https://repositorio-aberto.up.pt/bitstream/10216/125665/2/378408.pdf ↩
Lope, D. J., & Dolgun, A. (2020). Measuring the inequality of accessible trams in Melbourne. Journal of Transport Geography, 83, 102657. https://doi.org/10.1016/j.jtrangeo.2020.102657 ↩
Tetzlaff, S. J. (2019). Thinking outside the box: Effects of environmental enrichment and rearing duration on head-starting success of box turtles (Doctoral dissertation, University of Illinois at Urbana-Champaign) https://bit.ly/3eZwZA7 ↩
Wiscovitch-Russo, R., Rivera-Perez, J., Narganes-Storde, Y. M., García-Roldán, E., Bunkley-Williams, L., Cano, R., & Toranzos, G. A. (2020). Pre-Columbian zoonotic enteric parasites: An insight into Puerto Rican indigenous culture diets and life styles. PLOS ONE, 15(1), e0227810. https://doi.org/10.1371/journal.pone.0227810 ↩
Nüst, D., Eddelbuettel, D., Bennett, D., Cannoodt, R., Clark, D., Daroczi, G., … & Marwick, B. (2020). The Rockerverse: Packages and Applications for Containerization with R. arXiv preprint arXiv:2001.10641 https://arxiv.org/pdf/2001.10641.pdf ↩
Pérez-Goya, U., Montesino-SanMartin, M., Militino, A. F., & Ugarte, M. D. (2020). RGISTools: Downloading, Customizing, and Processing Time Series of Remote Sensing Data in R. arXiv preprint arXiv:2002.01859 https://arxiv.org/pdf/2002.01859.pdf ↩
Senior, S. (2020, February 4). Does Sure Start spending improve school readiness? An ecological longitudinal study. https://doi.org/10.31235/osf.io/rbcz5 ↩
Mooney, A., Conde, D. A., Healy, K., & Buckley, Y. M. (2020). A system wide approach to managing zoo collections for visitor attendance and in situ conservation. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-14303-2 ↩
Gagné, T. O., Reygondeau, G., Jenkins, C. N., Sexton, J. O., Bograd, S. J., Hazen, E. L., & Van Houtan, K. S. (2020). Towards a global understanding of the drivers of marine and terrestrial biodiversity. PLOS ONE, 15(2), e0228065. https://doi.org/10.1371/journal.pone.0228065 ↩
Gomez Isaza, D. F., Cramp, R. L., & Franklin, C. E. (2020). Living in polluted waters: A meta-analysis of the effects of nitrate and interactions with other environmental stressors on freshwater taxa. Environmental Pollution, 114091. https://doi.org/10.1016/j.envpol.2020.114091 ↩
Vílchez-Román, C., Huamán-Delgado, F., & Alhuay-Quispe, J. (2020). Social dimension activates the usage and academic impact of Open Access publications in Andean countries: a structural modeling-based approach. Information Development, 026666692090184. https://doi.org/10.1177/0266666920901849 ↩
Caseys, C., Gongjun Shi, Nicole Soltis, Raoni Gwinner, Jason Corwin, Susanna Atwell, Daniel Kliebenstein. 2020. Quantitative interactions drive Botrytis cinerea disease outcome across the plant kingdom. bioRxiv preprint 507491; doi: https://doi.org/10.1101/507491 ↩
Van Zonneveld, M., Rakha, M., Tan, S. yee, Chou, Y.-Y., Chang, C.-H., Yen, J.-Y., … Solberg, S. Ø. (2020). Mapping patterns of abiotic and biotic stress resilience uncovers conservation gaps and breeding potential of Vigna wild relatives. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-58646-8 ↩
Kim, J., Yoon, S., & Nam, D. (2020). netGO: R-Shiny package for network-integrated pathway enrichment analysis. Bioinformatics. https://doi.org/10.1093/bioinformatics/btaa077 ↩
Callanan, J., Stockdale, S. R., Shkoporov, A., Draper, L. A., Ross, R. P., & Hill, C. (2020). Expansion of known ssRNA phage genomes: From tens to over a thousand. Science Advances, 6(6), eaay5981. https://doi.org/10.1126/sciadv.aay5981 ↩
Mattatia, I. 2020. An empirical assessment of the extent to which the realized niche of bird species is truncated. Masters Thesis. University of Lausanne. https://bit.ly/2W0Nu6o ↩
CRAN: GitHub:
v0.9.0) of rplos is on CRAN - Interface to the Search API for Public Library of Science journals. See the release notes for changes. Checkout the vignettes to get started. v0.3.2) of crminer is on CRAN - Fetch scholarly full text from Crossref. See the release notes for changes. Checkout the README to get started. v0.9.2) of geojsonio is on CRAN - Convert Data from and to GeoJSON or TopoJSON. See the release notes for changes. Checkout the vignettes to get started. v0.9.6) of rnoaa is on CRAN - NOAA Weather Data from R. See the release notes for changes. Checkout the vignettes to get started. v0.3.2) of scrubr is on CRAN - clean biological occurrence records. See the release notes for changes. Checkout the docs to get started. v2.0.5) of ijtiff is on CRAN - Comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started. v0.3.8) of rdefra is on CRAN - get data from DEFRA’s UK-AIR website https://uk-air.defra.gov.uk/. See the release notes for changes. Checkout the rdefra vignette to get started. v0.5.2) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. v4.9.2.1) of plotly is on CRAN - Create Interactive Web Graphics via plotly.js. See the release notes for changes. Checkout the plotly book to get started. v0.4.1) of auk is on CRAN - eBird data extraction and processing. See the release notes for changes. Checkout the docs to get started. v0.3.8) of jstor is on CRAN - read data from JSTOR/DfR. See the release notes for changes. Checkout the docs to get started. v1.0) of tradestatistics is on CRAN - open trade statistics api wrapper and utility program. See the release notes for changes. Checkout the docs to get started. v1.4) of xslt is on CRAN - extensible style-sheet language transformations. See the release notes for changes. Checkout the README to get started. v1.1) of lightr is on CRAN - read spectrometric data and metadata. See the release notes for changes. Checkout the docs to get started. v0.9.94) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started. v0.5.4) of vcr is on CRAN - record HTTP calls to disk for test caching. See the release notes for changes. Checkout the HTTP testing book to get started. In the interest of reducing load on reviewers and editors as we manage the COVID-19 crisis, rOpenSci is temporarily pausing new submissions for software peer review. Please check back at our software review repository after 17 April for updates. In this period new submissions will not be handled, nor new reviewers assigned. Reviews and responses to reviews will be handled on a ‘best effort’ basis, but no follow-up reminders will be sent. Other rOpenSci community activities continue. We express our continued great appreciation for the work of our authors and reviewers.
Stefanie Butland and Maëlle Salmon wrote a post on lessons learned from creating the new blog guide: 10 Things We Learned in Creating the Blog Guide with bookdown
The following 21 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
A new use case was reported in the forum recently:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had eight recent examples of maintainer transitions within rOpenSci:
We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.
We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.
Cirtwill, A. R., Dalla Riva, G. V., Baker, N. J., Ohlsson, M., Norström, I., Wohlfarth, I., … Stouffer, D. B. (2020). Related plants tend to share pollinators and herbivores, but strength of phylogenetic signal varies among plant families. New Phytologist. https://doi.org/10.1111/nph.16420 ↩
Léveillé-Bourret, É., Chen, B.-H., Garon-Labrecque, M.-È., Ford, B. A., & Starr, J. R. (2020). RAD sequencing resolves the phylogeny, taxonomy and biogeography of Trichophoreae despite a recent rapid radiation (Cyperaceae). Molecular Phylogenetics and Evolution, 145, 106727. https://doi.org/10.1016/j.ympev.2019.106727 ↩
Moudrý, V., & Devillers, R. (2020). Quality and usability challenges of global marine biodiversity databases: An example for marine mammal data. Ecological Informatics, 56, 101051. https://doi.org/10.1016/j.ecoinf.2020.101051 ↩
Deng, H., Wang, Q., Turner, D. P., Sexton, K. E., Burns, S. M., Eikermann, M., … Houle, T. T. (2020). Sentiment analysis of real-world migraine tweets for population research. Cephalalgia Reports, 3, 251581631989886. https://doi.org/10.1177/2515816319898867 ↩
Shan, S., Soltis, P. S., Soltis, D. E., & Yang, B. (2020). Considerations in adapting CRISPR/Cas9 in nongenetic model plant systems. Applications in Plant Sciences, 8(1). https://doi.org/10.1002/aps3.11314 ↩
Horne, C. R., Hirst, A. G., & Atkinson, D. (2020). Selection for increased male size predicts variation in sexual size dimorphism among fish species. Proceedings of the Royal Society B: Biological Sciences, 287(1918), 20192640. https://doi.org/10.1098/rspb.2019.2640 ↩
Akpınar, B. A., Carlson, P. O., Paavilainen, V. O., & Dunn, C. D. (2020). Pathogenicity of human mtDNA variants is revealed by combining a novel phylogenetic analysis with machine learning. https://doi.org/10.1101/2020.01.10.902239 ↩
Milla, R., Bastida, J. M., Turcotte, M. M., Jones, G., Violle, C., Osborne, C. P., … Byun, C. (2018). Phylogenetic patterns and phenotypic profiles of the species of plants and mammals farmed for food. Nature Ecology & Evolution, 2(11), 1808–1817. https://doi.org/10.1038/s41559-018-0690-4 ↩
Scherer, C., Radchuk, V., Franz, M., Thulke, H., Lange, M., Grimm, V., & Kramer‐Schadt, S. (2020). Moving infections: individual movement decisions drive disease persistence in spatially structured landscapes. Oikos. https://doi.org/10.1111/oik.07002 ↩
Burns, M. D., & Bloom, D. D. (2020). Migratory lineages rapidly evolve larger body sizes than non-migratory relatives in ray-finned fishes. Proceedings of the Royal Society B: Biological Sciences, 287(1918), 20192615. https://doi.org/10.1098/rspb.2019.2615 ↩
Santos, J. C. (2020). Phylogenetic Analyses of Chemokine Receptors from Sequence Retrieval to Phylogenetic Trees. In Immune Mediators in Cancer (pp. 313-343). Humana, New York, NY. https://link.springer.com/protocol/10.1007/978-1-0716-0247-8_27 ↩
Walczyńska, A., Gudowska, A., & Sobczyk, Ł. (2020). Should I shrink or should I flow? – body size adjustment to thermo-oxygenic niche. https://doi.org/10.1101/2020.01.14.905901 ↩
Mathes, S. (2019). The Dynamics of Residential Sorting and Health: Implications of Climate Change in the US. https://sophiemathescom.files.wordpress.com/2019/11/job_market_paper_sophie_mathes-1.pdf ↩
Théroux-Rancourt, G., Roddy, A. B., Earles, J. M., Gilbert, M. E., Zwieniecki, M. A., Boyce, C. K., … Brodersen, C. R. (2020). Maximum CO2 diffusion inside leaves is limited by the scaling of cell size and genome size. https://doi.org/10.1101/2020.01.16.904458 ↩
Lakicevic M., Povak N., Reynolds K.M. (2020) Creating Maps. In: Introduction to R for Terrestrial Ecology. Springer, Cham https://link.springer.com/chapter/10.1007/978-3-030-27603-4_3 ↩
Wraith, J., Norman, P., & Pickering, C. (2020). Orchid conservation and research: An analysis of gaps and priorities for globally Red Listed species. Ambio. https://doi.org/10.1007/s13280-019-01306-7 ↩
Vincent, F., & Bowler, C. (2020). Diatoms Are Selective Segregators in Global Ocean Planktonic Communities. mSystems, 5(1). https://doi.org/10.1128/msystems.00444-19 ↩
Sawa, T., Momiyama, K., Mihara, T., Kainuma, A., Kinoshita, M., & Moriyama, K. (2020). Molecular epidemiology of clinically high‐risk Pseudomonas aeruginosa strains: Practical overview. Microbiology and Immunology. https://doi.org/10.1111/1348-0421.12776 ↩
Yuan, M. L., Jung, C., Wake, M. H., & Wang, I. J. (2020). Habitat use, interspecific competition and phylogenetic history shape the evolution of claw and toepad morphology in Lesser Antillean anoles. Biological Journal of the Linnean Society, 129(3), 630–643. https://doi.org/10.1093/biolinnean/blz203 ↩
Gilbertson, M. L. J., White, L. A., & Craft, M. E. (2020). Trade‐offs with telemetry‐derived contact networks for infectious disease studies in wildlife. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13355 ↩
Bachman, S., Walker, B., Barrios, S., Copeland, A., & Moat, J. (2020). Rapid Least Concern: towards automating Red List assessments. Biodiversity Data Journal, 8. https://doi.org/10.3897/bdj.8.e47018 ↩
CRAN: GitHub:
parzer (v0.1.4) is on CRAN - parse messy geographic coordinates. Checkout the docs to get started. v0.1.13) of spatsoc is on CRAN - detecting spatial and temporal groups in GPS relocations. See the release notes for changes. Checkout the docs to get started. v0.2.9) of ropenaq is on CRAN - Air quality data from the open data platform OpenAQ. See the release notes for changes. Checkout the docs to get started. v7.12.0) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started. v1.0.2) of plater is on CRAN - read, tidy, and display data from microtiter plates. See the release notes for changes. Checkout the docs to get started. v0.6.2) of webmockr is on CRAN - stubbing and setting expectations on HTTP requests. See the release notes for changes. Checkout the HTTP testing book to get started. v0.0.7) of plotdap is on CRAN - easily visualize data from ERDDAP servers via the rerddap package. See the release notes for changes. Checkout the vignette to get started. v0.9.93) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started. v1.0.0) of rcrossref is on CRAN - R client for the Crossref API. See the release notes for changes. Checkout the docs to get started. v0.2.0) of rbraries is on CRAN - interface to the Libraries.io API. See the release notes for changes. Checkout the docs to get started. v1.3.1) of UCSCXenaTools is on CRAN - download and explore datasets from UCSC Xena data hubs. See the release notes for changes. Checkout the docs to get started. In the interest of reducing load on reviewers and editors as we manage the COVID-19 crisis, rOpenSci is temporarily pausing new submissions for software peer review. Please check back at our software review repository after 17 April for updates. In this period new submissions will not be handled, nor new reviewers assigned. Reviews and responses to reviews will be handled on a ‘best effort’ basis, but no follow-up reminders will be sent. Other rOpenSci community activities continue. We express our continued great appreciation for the work of our authors and reviewers.
Scott Chamberlain wrote a post on the new parzer package: parzer: Parse Messy Geographic Coordinates.
The following 23 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
The R-Journal is seeking reviewers - checkout the forum thread for more.
A new use case was reported in the forum recently:
python: Python 101: Learning About Lists testing: Necessary & Sufficient Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had eight recent examples of maintainer transitions within rOpenSci:
We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.
We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.
Hsu, C. W. (2019). Disparities in public charging infrastructure deployment and inequitable electric vehicle ownership cost based on income and race (Doctoral dissertation, Humboldt State University). http://bit.ly/2MQDAAF ↩
Fatikhunnada, A., Liyantono, Solahudin, M., Buono, A., Kato, T., & Seminar, K. B. (2020). Assessment of pre-treatment and classification methods for Java paddy field cropping pattern detection on MODIS images. Remote Sensing Applications: Society and Environment, 17, 100281. https://doi.org/10.1016/j.rsase.2019.100281 ↩
Hansen, O. L. P., Svenning, J., Olsen, K., Dupont, S., Garner, B. H., Iosifidis, A., … Høye, T. T. (2019). Species‐level image classification with convolutional neural network enables insect identification from habitus images. Ecology and Evolution, 10(2), 737–747. https://doi.org/10.1002/ece3.5921 ↩
Kovalenko, Y. (2019). Stop and smell the grapes : altering cultivar-typical aromas in Gewürztraminer (Vitis vinifera L.) berries via regulated deficit irrigation and crop load management (T). University of British Columbia. https://open.library.ubc.ca/cIRcle/collections/ubctheses/24/items/1.0387322 ↩
Mienna, I. M., Speed, J. D. M., Bendiksby, M., Thornhill, A. H., Mishler, B. D., & Martin, M. D. (2019). Differential patterns of floristic phylogenetic diversity across a post‐glacial landscape. Journal of Biogeography. https://doi.org/10.1111/jbi.13789 ↩
Asevedo, L., D’Apolito, C., Misumi, S. Y., Barros, M. A. de, Barth, O. M., & Avilla, L. dos S. (2020). Palynological analysis of dental calculus from Pleistocene proboscideans of southern Brazil: A new approach for paleodiet and paleoenvironmental reconstructions. Palaeogeography, Palaeoclimatology, Palaeoecology, 540, 109523. https://doi.org/10.1016/j.palaeo.2019.109523 ↩
Milà, C., Curto, A., Dimitrova, A., Sreekanth, V., Kinra, S., Marshall, J. D., & Tonne, C. (2020). Identifying predictors of personal exposure to air temperature in peri-urban India. Science of The Total Environment, 707, 136114. https://doi.org/10.1016/j.scitotenv.2019.136114 ↩
Nguyen, V. T., Dietrich, J., & Uniyal, B. (2020). Modeling interbasin groundwater flow in karst areas: Model development, application, and calibration strategy. Environmental Modelling & Software, 124, 104606. https://doi.org/10.1016/j.envsoft.2019.104606 ↩
Torregroza-Espinosa, A. C., Restrepo, J. C., Correa-Metrio, A., Hoyos, N., Escobar, J., Pierini, J., & Martínez, J.-M. (2020). Fluvial and oceanographic influences on suspended sediment dispersal in the Magdalena River Estuary. Journal of Marine Systems, 204, 103282. https://doi.org/10.1016/j.jmarsys.2019.103282 ↩
Akpoti, K., Kabo-bah, A. T., Dossou-Yovo, E. R., Groen, T. A., & Zwart, S. J. (2020). Mapping suitability for rice production in inland valley landscapes in Benin and Togo using environmental niche modeling. Science of The Total Environment, 709, 136165. https://doi.org/10.1016/j.scitotenv.2019.136165 ↩
Mingione, M., Cristofaro, M., & Mondi, D. (2020). If I give you my emotion, what do I get? Conceptualizing and measuring the co-created emotional value of the brand. Journal of Business Research, 109, 310–320. https://doi.org/10.1016/j.jbusres.2019.11.071 ↩
D’Amen, M., & Azzurro, E. (2019). Integrating univariate niche dynamics in species distribution models: A step forward for marine research on biological invasions. Journal of Biogeography, 47(3), 686–697. https://doi.org/10.1111/jbi.13761 ↩
Meng, S., Zhan, S., Dou, W., & Ge, W. (2019). The interactome and proteomic responses of ALKBH7 in cell lines by in-depth proteomics analysis. Proteome Science, 17(1). https://doi.org/10.1186/s12953-019-0156-x ↩
Czernecki, B., Głogowski, A., & Nowosad, J. (2020). Climate: An R Package to Access Free In-Situ Meteorological and Hydrological Datasets For Environmental Assessment. Sustainability, 12(1), 394. https://doi.org/10.3390/su12010394 ↩
Shi, L., Tian, H., Wang, P., Li, L., Zhang, Z., Zhang, J., & Zhao, Y. (2020). Spaceflight and simulated microgravity suppresses macrophage development via altered RAS/ERK/NFκB and metabolic pathways. Cellular & Molecular Immunology. https://doi.org/10.1038/s41423-019-0346-6 ↩
Lestina, F. Trends in US Foreign Policy Prioritizations, 2000–2019. Proceedings of the 53rd Hawaii International Conference on System Sciences. https://scholarspace.manoa.hawaii.edu/bitstream/10125/63832/0074.pdf ↩
Quintero, E., Pizo, M. A., & Jordano, P. (2020). Fruit resource provisioning for avian frugivores: The overlooked side of effectiveness in seed dispersal mutualisms. Journal of Ecology. https://doi.org/10.1111/1365-2745.13352 ↩
Blowes, S. A., Chase, J. M., Di Franco, A., Frid, O., Gotelli, N. J., Guidetti, P., … Belmaker, J. (2020). Mediterranean marine protected areas have higher biodiversity via increased evenness, not abundance. Journal of Applied Ecology, 57(3), 578–589. https://doi.org/10.1111/1365-2664.13549 ↩
Wunderlich, F., & Memmert, D. (2020). Innovative Approaches in Sports Science—Lexicon-Based Sentiment Analysis as a Tool to Analyze Sports-Related Twitter Communication. Applied Sciences, 10(2), 431. https://doi.org/10.3390/app10020431 ↩
Nguyen, H. N., Hung, C.-M., Yang, M.-Y., & Lin, S.-M. (2020). Sympatric competitors have driven the evolution of temporal activity patterns in Cnemaspis geckos in Southeast Asia. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-019-56549-x ↩
Carta, A., Bedini, G., & Peruzzi, L. (2020). A deep dive into the ancestral chromosome number of flowering plants. bioRxiv preprint. https://doi.org/10.1101/2020.01.05.893859 ↩
Alves, D. M. C. C., Eduardo, A. A., da Silva Oliveira, E. V., Villalobos, F., Dobrovolski, R., Pereira, T. C., … Gouveia, S. F. (2020). Unveiling geographical gradients of species richness from scant occurrence data. Global Ecology and Biogeography, 29(4), 748–759. https://doi.org/10.1111/geb.13055 ↩
Jaric, I., & Djeric, M. (2019). Curriculum and labor market: Comparative analysis of the curricular outcomes of the study program in sociology at the Faculty of Philosophy, University of Belgrade and the required competences in the labor market. Sociologija, 61(Suppl. 1), 718–741. https://doi.org/10.2298/soc19s1718j ↩
CRAN: GitHub:
v0.1.0) of ghql is on CRAN - general purpose GraphQL client. Checkout the docs to get started. v0.3.0) of crminer is on CRAN - Fetch scholarly full text from Crossref. See the release notes for changes. Checkout the README to get started. v0.1.1) of rromeo is on CRAN - access publisher copyright & self-archiving policies via the SHERPA/RoMEO API. See the release notes for changes. Checkout the docs to get started. v1.1.0) of cyphr is on CRAN - high level encryption wrappers. See the release notes for changes. Checkout the docs to get started. v2.2.0) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the occurrence manual to get started. v0.1.5) of baRcodeR is on CRAN - label creation for tracking and collecting data from biological samples. See the release notes for changes. Checkout the docs to get started. v1.3) of hydroscoper is on CRAN - interface to the Greek National Data Bank for Hydrological and Meteorological Information http://www.hydroscope.gr/. See the release notes for changes. Checkout the vignettes to get started. v1.1.1) of MODISTools is on CRAN - interface to the MODIS Land Products Subsets web services. See the release notes for changes. Checkout the docs to get started. v0.5.2) of rdatacite is on CRAN - client for DataCite. See the release notes for changes. Checkout the README to get started. v0.5.0) of vcr is on CRAN - record HTTP calls to disk for test caching. See the release notes for changes. Checkout the HTTP testing book to get started. v1.2.0) of stats19 is on CRAN - Work with Open Road Traffic Casualty Data from Great Britain. See the release notes for changes. Checkout the docs to get started. v0.2.1) of git2rdata is on CRAN - store and retrieve data.frames in a Git repository. See the release notes for changes. Checkout the docs to get started. v0.4.3) of nomisr is on CRAN - access UK official statistics from the Nomis database. See the release notes for changes. Checkout the docs to get started. v0.5.0) of webchem is on CRAN - Chemical information from the web. See the release notes for changes. Checkout the docs to get started. v0.6.0) of webmockr is on CRAN - stubbing and setting expectations on HTTP requests. See the release notes for changes. Checkout the HTTP testing book to get started. We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following package was recently submitted:
Steffi LaZerte wrote a post on our next community call: Community Call - Maintaining an R Package.
Patrick Schratz wrote a post on using Github Actions with the tic package: Supercharge your GitHub Actions Experience with tic. tic works with many continuous integration (CI) services.
The following 17 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
Emilio Bruna asked recently: What is best practice when a dependency is removed from CRAN?
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had eight recent examples of maintainer transitions within rOpenSci:
We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.
We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.
van der Loo, M. P., & de Jonge, E. (2019). Data Validation Infrastructure for R. arXiv preprint arXiv:1912.09759. https://arxiv.org/pdf/1912.09759.pdf ↩
Marshall, B. M., & Strine, C. T. (2019). Exploring snake occurrence records: Spatial biases and marginal gains from accessible social media. PeerJ, 7, e8059. https://doi.org/10.7717/peerj.8059 ↩
Cameron, J. (2019). Improving passive acoustic monitoring methods for anuran amphibians in northern Alberta, Canada. https://era.library.ualberta.ca/items/82cf4970-7243-49cc-88ac-cbef893cd062 ↩
Pontes, L. F. V. A. (2019). Biodiversity informatics-entomological data processing, analysis and visualization (Doctoral dissertation) https://repositorio.ul.pt/bitstream/10451/40544/1/ulfc125176_tm_Leonor_Pontes.pdf ↩
Tancoigne, E. (2019). Invisible brokers: “citizen science” on Twitter. Journal of Science Communication, 18(06). https://doi.org/10.22323/2.18060205 ↩
Hosford, K., & Winters, M. 2019. Quantifying the Bicycle Share Gender Gap. Transport Findings, November. https://doi.org/10.32866/10802 ↩
Noecker, C., Chiu, H. C., McNally, C. P., & Borenstein, E. (2019). Defining and evaluating microbial contributions to metabolite variation in microbiome-metabolome association studies. mSystems, 4(6). https://doi.org/10.1128/mSystems.00579-19 ↩
Ruiz-Sanchez, E., Maya-Lastra, C. A., Steinmann, V. W., Zamudio, S., Carranza, E., Murillo, R. M., & Rzedowski, J. (2019). Datataxa: a new script to extract metadata sequence information from GenBank, the Flora of Bajío as a case study. Botanical Sciences, 97(4), 754–760. https://doi.org/10.17129/botsci.2226 ↩
Greenhalgh, S. P., Willet, K. B. S., & Koehler, M. J. (2019). Approaches to Mormon Identity and Practice in the #ldsconf Twitter Hashtag. Journal of Media and Religion, 18(4), 122–133. https://doi.org/10.1080/15348423.2019.1696121 ↩
Die, J. V., Elmassry, M. M., LeBlanc, K. H., Awe, O. I., Dillman, A., & Busby, B. (2018). GeneHummus: A pipeline to define gene families and their expression in legumes and beyond. https://doi.org/10.1101/436659 ↩
Maia, R., Gruson, H., Endler, J. A., & White, T. E. (2018). pavo 2: new tools for the spectral and spatial analysis of colour in R. https://doi.org/10.1101/427658 ↩
Mowinckel, A. M., & Vidal-Piñeiro, D. (2019). Visualisation of Brain Statistics with R-packages ggseg and ggseg3d. arXiv preprint arXiv:1912.08200 https://arxiv.org/abs/1912.08200 ↩
Champagne, E., Royo, A. A., Tremblay, J.-P., & Raymond, P. (2019). Phytochemicals Involved in Plant Resistance to Leporids and Cervids: a Systematic Review. Journal of Chemical Ecology, 46(1), 84–98. https://doi.org/10.1007/s10886-019-01130-z ↩
Burrows, M. T., Hawkins, S. J., Moore, J. J., Adams, L., Sugden, H., Firth, L., & Mieszkowska, N. (2020). Global‐scale species distributions predict temperature‐related changes in species composition of rocky shore communities in Britain. Global Change Biology, 26(4), 2093–2105. https://doi.org/10.1111/gcb.14968 ↩
Avdeev, S. (2019). International Collaboration In Higher Education Research: A Gravity Model Approach. Higher School of Economics Research Paper No. WP BRP, 54. https://wp.hse.ru/data/2019/12/18/1523102390/54EDU2019.pdf ↩
Herrera, C. M. (2020). Flower traits, habitat, and phylogeny as predictors of pollinator service: a plant community perspective. Ecological Monographs. https://doi.org/10.1002/ecm.1402 ↩
Kim, H. M., Jo, J., Park, C., Choi, B.-J., Lee, H.-G., & Kim, K. Y. (2019). Epibionts associated with floating Sargassum horneri in the Korea Strait. ALGAE, 34(4), 303–313. https://doi.org/10.4490/algae.2019.34.12.10 ↩
CRAN: GitHub:
v0.2.8) of osfr is on CRAN - interface to the Open Science Framework (OSF). See the release notes for changes. Checkout the docs to get started. v0.1.0) of taxadb is on CRAN - a local taxonomic database interface. Checkout the docs to get started. v0.1.0) of outsider.base is on CRAN - base package for outsider. Checkout the docs to get started. v1.0.3) of cyphr is on CRAN - high level encryption wrappers. See the release notes for changes. Checkout the docs to get started. fix test for stringsAsFactors change for R v4
v0.2.1) of git2rdata is on CRAN - store and retrieve data.frames in a Git repository. See the release notes for changes. Checkout the docs to get started. fix examples and tests for stringsAsFactors change for R v4
v0.5.0) of webchem is on CRAN - Chemical information from the web. See the release notes for changes. Checkout the docs to get started. new data sources; many bug fixes
v0.6.0) of webmockr is on CRAN - stubbing and setting expectations on HTTP requests. See the release notes for changes. Checkout the HTTP testing book to get started. improved function reference in docs site; fixes for JSON encoded body requests; many other fixes
v7.11.0) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started. allow dynamic files; many improvements and bug fixes
v1.1.2) of lingtypology is on CRAN - linguistic typology and mapping. See the release notes for changes. Checkout the docs to get started. many parameter name changes across functions; fixes for stringsAsFactors change for R v4
v2.4.3) of RNeXML is on CRAN - Semantically Rich I/O for the NeXML Format. See the release notes for changes. Checkout the docs to get started. fix tests for stringsAsFactors change for R v4
v0.5.1) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. fixes for stringsAsFactors change for R v4
v1.3.0) of UCSCXenaTools is on CRAN - download and explore datasets from UCSC Xena data hubs. See the release notes for changes. Checkout the docs to get started. added two new data hubs; improved a function
v2.3.5) of beautier is on CRAN - create BEAST2 input files programmatically. See the release notes for changes. Checkout the docs to get started. gains 4 new functions, renames a few functions
v0.0.11) of piggyback is on CRAN - Managing larger data on a GitHub repository. See the release notes for changes. Checkout the docs to get started.
guess_repo()now infers a remote when there are multiple remotes; fixes torelease_info()andpb_info()
v0.3.3) of taxa is on CRAN - taxonomic classes for groupings of taxonomic names without data, and those with data. See the release notes for changes. Checkout the docs to get started. numeric column names in tables in taxmap are now supported; bug fixes
v3.1.2) of qualtRics is on CRAN - download Qualtrics survey data. See the release notes for changes. Checkout the docs to get started. 5 functions deprecated; now using updated version of Qualtrics API
v1.1.0) of dbparser is on CRAN - DrugBank database XML parser. See the release notes for changes. Checkout the docs to get started. complete overhaul of exported function names
v0.4.0) of isdparser is on CRAN - parse NOAA Integrated Surface data files. See the release notes for changes. Checkout the docs to get started. new function
isd_parse_csv()to work with ISD csv files
v0.0.6) of plotdap is on CRAN - easily visualize data from ERDDAP servers via the rerddap package. See the release notes for changes. Checkout the vignette to get started. fixed problem when no time coordinate in dataset;
add_tabledap()overlays on gridded maps now work for ggplot2
We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following package was recently submitted:
The following package recently went through our software-review process and has been approved:
It’s time for another installment of … 2 Months in 2 Minutes - rOpenSci News, February 2020 - if you want a brief summary of the last 2 months of these newsletters, these blog posts are for you (written by Stefanie Butland)
Julia Stewart Lowndes cross-posted a blog post on our blog: rOpenSci’s Leadership in #rstats Culture. In it she reflects on her experience at the 2020 RStudio conference as well as her experience at the 2015 rOpenSci Unconference.
Software Review:
Malcom Morgan wrote about his recently rOpenSci reviewed package opentripplanner: opentripplanner: Fast and Easy Multimodal Trip Planning in R with OpenTripPlanner. Malcom discusses the design of the package, and how to use opentripplanner.
![](\"../assets/img/logo_opentripplanner.png\"){kind=logo}
The following 15 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
Peter Desmet asked a good question that many R package maintainers run in to: What if raw data in package is too large?
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had six recent examples of maintainer transitions within rOpenSci:
We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.
Godfrey, J. M., Riggio, J., Orozco, J., Guzmán‐Delgado, P., Chin, A. R. O., & Zwieniecki, M. A. (2020). Ray fractions and carbohydrate dynamics of tree species along a 2750 m elevation gradient indicate climate response, not spatial storage limitation. New Phytologist, 225(6), 2314–2330. https://doi.org/10.1111/nph.16361 ↩
Zhong, B. (2019). Towards Developing a Double Cropping System Between Winter Barley and Soybean in the Upper Midwest. http://bit.ly/3co35Es ↩
Betts, M. G., Wolf, C., Pfeifer, M., Banks-Leite, C., Arroyo-Rodríguez, V., Ribeiro, D. B., … Ewers, R. M. (2019). Extinction filters mediate the global effects of habitat fragmentation on animals. Science, 366(6470), 1236–1239. https://doi.org/10.1126/science.aax9387 ↩
Kim, K. W., Allen, D. W., Briese, T., Couper, J. J., Barry, S. C., … Colman, P. G. (2020). Higher frequency of vertebrate‐infecting viruses in the gut of infants born to mothers with type 1 diabetes. Pediatric Diabetes, 21(2), 271–279. https://doi.org/10.1111/pedi.12952 ↩
Atalah, J., & Forrest, B. (2019). Forecasting mussel settlement using historical data and boosted regression trees. Aquaculture Environment Interactions, 11, 625–638. https://doi.org/10.3354/aei00337 ↩
Karakülah, G., Arslan, N., Yandım, C., & Suner, A. (2019). TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model. PeerJ, 7, e8192. https://doi.org/10.7717/peerj.8192 ↩
Yusri, S., Siregar, V. P., & Suharsono. (2019). Distribution Modelling of Porites (Poritidae) in Indonesia. IOP Conference Series: Earth and Environmental Science, 363, 012025. https://doi.org/10.1088/1755-1315/363/1/012025 ↩
Clark, T. J., & Luis, A. D. (2019). Nonlinear population dynamics are ubiquitous in animals. Nature Ecology & Evolution, 4(1), 75–81. https://doi.org/10.1038/s41559-019-1052-6 ↩
Ekroos, J., Kleijn, D., Batáry, P., Albrecht, M., Báldi, A., Blüthgen, N., … Smith, H. G. (2020). High land-use intensity in grasslands constrains wild bee species richness in Europe. Biological Conservation, 241, 108255. https://doi.org/10.1016/j.biocon.2019.108255 ↩
Lysne, V. (2019). Biomarkers of one-carbon metabolism and B-vitamin status: Targeted metabolomics in rats and humans exploring the effects of PPARα-activation and dietary composition. http://bit.ly/3crBane ↩
Vitale, O., Preste, R., Palmisano, D., & Attimonelli, M. (2019). A data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information. Molecular Genetics & Genomic Medicine, 8(2). https://doi.org/10.1002/mgg3.1085 ↩
Wcisel, D. J., III, J. T. H., Yoder, J. A., & Dornburg, A. (preprint) Transcriptome Ortholog Alignment Sequence Tools (TOAST) for Phylogenomic Dataset Assembly. https://doi.org/10.21203/rs.2.16269/v3 ↩
Sansone, A., Cignarelli, A., Ciocca, G., Pozza, C., Giorgino, F., Romanelli, F., & Jannini, E. A. (2019). The Sentiment Analysis of Tweets as a New Tool to Measure Public Perception of Male Erectile and Ejaculatory Dysfunctions. Sexual Medicine, 7(4), 464–471. https://doi.org/10.1016/j.esxm.2019.07.001 ↩
Finnegan, A., Sao, S. S., & Huchko, M. J. (2019). Using a Chord Diagram to Visualize Dynamics in Contraceptive Use: Bringing Data Into Practice. Global Health: Science and Practice, 7(4), 598–605. https://doi.org/10.9745/ghsp-d-19-00205 ↩
Kim, J., Plitman, E., Iwata, Y., Nakajima, S., Mar, W., Patel, R., … Graff-Guerrero, A. (2020). Neuroanatomical profiles of treatment-resistance in patients with schizophrenia spectrum disorders. Progress in Neuro-Psychopharmacology and Biological Psychiatry, 99, 109839. https://doi.org/10.1016/j.pnpbp.2019.109839 ↩
CRAN: GitHub:
v0.9.0) of geojsonio is on CRAN - Convert Data from and to GeoJSON or TopoJSON. See the release notes for changes. Checkout the vignettes to get started.
geojson_sf()/geojson_sp()now accept strings; replace httr with crul & rgdal replaced with sf
v0.4.0) of geojsonlint is on CRAN - Tools for Validating GeoJSON. See the release notes for changes. Checkout the docs to get started.
geojson_lint()defunct - the geojsonlint.com API is down
v2.1.0) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the occurrence manual to get started.
occ_download()bug fix forwithinpredicates for geometry queries;occ_spellcheck()now defunct
v4.9.2) of plotly is on CRAN - Create Interactive Web Graphics via plotly.js. See the release notes for changes. Checkout the plotly book to get started. upgrade plotly.js to v1.52.2
v0.9.92) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started. all Catalogue of Life functions removed (get in touch if you need help); new fxn
gn_parse()for Global Names name parser
v1.0.8) of spocc is on CRAN - an interface to many species occurrence data sources. See the release notes for changes. Checkout the docs to get started. v1.1.1) of lingtypology is on CRAN - linguistic typology and mapping. See the release notes for changes. Checkout the docs to get started. update glottolog from v2.7 to v4.1; some fxns removed
v0.3.0) of scrubr is on CRAN - clean biological occurrence records. See the release notes for changes. Checkout the docs to get started. new fxn
fix_names(); new fxneco_regionto filter data by ecoregions; new fxnscoord_imprecise()/coord_uncertain()to clean coordinates
v1.0.2) of fingertipsR is on CRAN - Fingertips data for public health http://fingertips.phe.org.uk/. See the release notes for changes. Checkout the vignettes to get started. bug fix for
fingertips_data()
v0.1.3) of osmdata is on CRAN - import OpenStreetMap data as simple features or spatial objects. See the release notes for changes. Checkout the docs to get started.
osmdata_pbf()function removed; remove deprecatedadd_feature()- replaced byadd_osm_feature()
v2.0.2) of EML is on CRAN - read and write ecological metadata language files. See the release notes for changes. Checkout the docs to get started. v0.4.1) of nlrx is on CRAN - setup, run and analyze NetLogo model simulations. See the release notes for changes. Checkout the vignettes to get started. v0.2.0.8) of opentripplanner is on CRAN - client for OpenTripPlanner for journey planning. See the release notes for changes. Checkout the docs to get started. v0.6.4) of rorcid is on CRAN - Interface to the Orcid.org API. See the release notes for changes. Checkout the vignette to get started.
recursiveparameter removed fromorcid();orcid_search()loses some parameters;orcid()gains additional fields to query, e.g.,peer-review-type
v2.7) of assertr is on CRAN - Assertive Programming for R Analysis Pipelines. See the release notes for changes. Checkout the vignette to get started. added “inverse” option to predicates
v0.4.0) of emld is on CRAN - ecological metadata as linked data. See the release notes for changes. Checkout the vignette to get started. fixed serialization bug in
referencesattribute; fixed validation bugs
v0.3.3) of weathercan is on CRAN - Download weather data from the Environment and Climate Change Canada website. See the release notes for changes. Checkout the docs to get started. update internal datasets
v1.7.7) of RSelenium is on CRAN - R client for Selenium Remote WebDriver. See the release notes for changes. Checkout the docs to get started. re-submission to CRAN after archiving
We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following packages were recently submitted:
![](\"../assets/img/ozunconf19-group.jpg\")
Software Review:
![](\"../assets/img/taxadb_logo.svg\"){kind=logo}
The following 13 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
Two use cases have been reported in the forum recently:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had six recent examples of maintainer transitions within rOpenSci:
We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.
Næss, M. W. (2019). From hunter-gatherers to nomadic pastoralists: forager bands do not tell the whole story of the evolution of human cooperation. https://doi.org/10.31235/osf.io/9c8bm ↩
Wang, S., He, Z., Wang, X., Li, H., & Liu, X.-S. (2019). Antigen presentation and tumor immunogenicity in cancer immunotherapy response prediction. eLife, 8. https://doi.org/10.7554/elife.49020 ↩
Thorson, J. T. (2019). Predicting recruitment density dependence and intrinsic growth rate for all fishes worldwide using a data‐integrated life‐history model. Fish and Fisheries. <https://doi.org/10.1111/faf.12427 ↩
Geary, W. L., Doherty, T. S., Nimmo, D. G., Tulloch, A. I. T., & Ritchie, E. G. (2020). Predator responses to fire: A global systematic review and meta‐analysis. Journal of Animal Ecology. https://doi.org/10.1111/1365-2656.13153 ↩
Hong, T., Xu, Y., Sun, K., Zhang, W., & Luo, X. (2019). Visualizing Urban Microclimate and Quantifying its Impact on Building Energy Use in San Francisco. Proceedings of the 1st ACM International Workshop on Urban Building Energy Sensing, Controls, Big Data Analysis, and Visualization - UrbSys’19. https://doi.org/10.1145/3363459.3363536 ↩
Lange, H., Ndecky, S. Y. A., Gomez-Diaz, C., Pflieger, D., Butel, N., Zumsteg, J., … Gagliardi, D. (2019). RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex in Arabidopsis. Nature Communications, 10(1). https://doi.org/10.1038/s41467-019-11807-4 ↩
Báez, J. C., Barbosa, A. M., Pascual, P., Ramos, M. L., & Abascal, F. (2019). Ensemble modeling of the potential distribution of the whale shark in the Atlantic Ocean. Ecology and Evolution, 10(1), 175–184. https://doi.org/10.1002/ece3.5884 ↩
Estrada-Peña, A., Nava, S., Tarragona, E., Bermúdez, S., de la Fuente, J., Domingos, A., … Guglielmone, A. A. (2019). Species occurrence of ticks in South America, and interactions with biotic and abiotic traits. Scientific Data, 6(1). https://doi.org/10.1038/s41597-019-0314-0 ↩
Lecocq, T., Benard, A., Pasquet, A., Nahon, S., Ducret, A., Dupont-Marin, K., … Thomas, M. (2019). TOFF, a database of traits of fish to promote advances in fish aquaculture. Scientific Data, 6(1). https://doi.org/10.1038/s41597-019-0307-z ↩
Reis, V. S. (2019). Uma perspectiva macroecológica sobre o risco de extinção em mamíferos. Thesis. http://bit.ly/38mfmHG ↩
Yagli, G. M., Yang, D., Gandhi, O., & Srinivasan, D. (2019). Can we justify producing univariate machine-learning forecasts with satellite-derived solar irradiance? Applied Energy, 114122. https://doi.org/10.1016/j.apenergy.2019.114122 ↩
Li, Y., Ge, D., & Lu, C. (2019). The SMART App: an interactive web application for comprehensive DNA methylation analysis and visualization. Epigenetics & Chromatin, 12(1). https://doi.org/10.1186/s13072-019-0316-3 ↩
Fu, D. Y., & Hughey, J. J. (2019). Releasing a preprint is associated with more attention and citations for the peer-reviewed article. eLife, 8. https://doi.org/10.7554/elife.52646 ↩
CRAN: GitHub:
v0.1.0) of crevents is on CRAN - client for the Crossref Events API. Checkout the docs to get started. v2.1.1) of babette is on CRAN - control BEAST2 from R. Checkout the docs to get started. This package recently went through rOpenSci software review. v7.10.0) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started. many new features and enhancements
v2.1) of skimr is on CRAN - compact and flexible summaries of data. See the release notes for changes. Checkout the vignettes to get started.
to_long()is now generic; works w/ new tibble version; fix toskimr::summarize()
v1.3) of cld3 is on CRAN - Bindings to Google’s Compact Language Detector 3. See the release notes for changes. Checkout the docs to get started. cran fix: do not use CXXCPP
v2.0.0) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the occurrence manual to get started. breaking changes:
occ_downloadinterface has changed; new fxnocc_download_wait()
v0.9.7) of rzmq is on CRAN - R Bindings for ZeroMQ, a lightweight messaging kernel. See the release notes for changes. Checkout the README to get started. cran fix: do not use CXXCPP
v0.2.5) of wdman is on CRAN - Webdriver/Selenium binary manager. See the release notes for changes. Checkout the vignette to get started. replaced
subprocess(archived in CRAN) withprocessx
v0.4.0 and v0.5.0) of av have hit CRAN since the last newsletter - working with audio and video. See the release notes for changes. Checkout the docs to get started, and the recent blog post by Jeroen. windows/mac binaries now ship w/ ffmpeg 4.2.2; new functions
v0.9.0) of rbhl is on CRAN - interface to the Biodiversity Heritage Library. See the release notes for changes. Checkout the docs to get started. package re-worked for new BHL API version; some functions defunct, some new functions
v2.4.2) of RNeXML is on CRAN - Semantically Rich I/O for the NeXML Format. See the release notes for changes. Checkout the vignettes to get started. minor bug fix
v0.8.0) of rvertnet is on CRAN - Search Vertnet, a database of vertebrate specimen records. See the release notes for changes. Checkout the docs to get started.
searchbyterm()&bigsearch()reworked: no more fuzzy arg matching
v0.6.0) of rorcid is on CRAN - Interface to the Orcid.org API. See the release notes for changes. Checkout the vignette to get started.
orcid_citations()parses bibtex better;orcid_search()gains new parameters & bug fixes
v0.6.0) of rredlist is on CRAN - IUCN Red List client. See the release notes for changes. Checkout the README to get started. note in docs wrt different result in website vs. package; fail with useful message when NA’s passed to functions
v1.0) of lightr is on CRAN - read spectrometric data and metadata. See the release notes for changes. Checkout the docs to get started. parallel processing now relies on the future package;
lr_parse_generic()now works with non-UTF8 files;lr_get_spec()w/ newinterpolateparam
v0.5.0) of microdemic is on CRAN - Microsoft Academic API client. See the release notes for changes. Checkout the README to get started. new author Christopher Baker; fix error messages
v0.5.0) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. some package dependencies removed;
route_graphhopper()now works w/ a local graphhopper instance; bug fixes
v0.4.0) of charlatan is on CRAN - a comprehensive approach to making fake data, supporting many languages. See the release notes for changes. Checkout the docs to get started. new vignette “contributing to charlatan”; some new locales
v2.0.1) of GSODR is on CRAN - Global Surface Summary of the Day (GSOD) Weather Data from R. See the release notes for changes. Checkout the docs to get started. requires R>3.5; tidy documentation; bug fixes
v2.3) of magick is on CRAN - Advanced graphics and Image-Processing in R. See the release notes for changes. Checkout the vignette to get started. fix crash with openmp on OSX;
image_shadowfix;image_animate()andimage_read()improvements
v1.0) of NLMR is on CRAN - Simulating neutral landscape models. See the release notes for changes. Checkout the docs to get started. v1.0.0) of pangaear is on CRAN - Client for the Pangaea database. See the release notes for changes. Checkout the docs to get started.
pg_search()fix for searching with a bounding box that crosses 180/-180 longitude
v0.7.0) of bomrang is on CRAN - Australian government Bureau of Meteorology (BOM) data. See the release notes for changes. Checkout the docs to get started. requires R>3.5; 3 new fxns to parse local XML files; bug fixes
v1.0.2) of cyphr is on CRAN - high level encryption wrappers. See the release notes for changes. Checkout the docs to get started. v1.4) of unrtf is on CRAN - Extract text from Rich Text Format (RTF) documents. See the release notes for changes. Checkout the README to get started. fix compiler warning on Windows GCC 8
v1.2.0) of c14bazAAR is on CRAN - download and prepare C14 dates from different source databases. See the release notes for changes. Checkout the docs to get started. unified database names throughout pkg; new fxns
v1.1.0) of elastic is on CRAN - general purpose interface to Elasticsearch. See the release notes for changes. Checkout the docs to get started. make
typeoptional in all functions; new methodindex_shrink(); fix to makedocs_bulk()with pipeline attachments work
v0.9.2) of biomartr is on CRAN - Genomic Data Retrieval. See the release notes for changes. Checkout the vignettes to get started. fix for examples run on CRAN
v0.2.3) of rdflib is on CRAN - high level wrapper around the redland rdf package. See the release notes for changes. Checkout the docs to get started. drop import of deprecated redland method
getNextResult
v0.6.0) of wellknown is on CRAN - Convert between WKT and GeoJSON. See the release notes for changes. Checkout the vignette to get started. fix to
wkt_wkb()method - support new version of V8 that converts JS buffers to raw vectors
v0.5.0) of gistr is on CRAN - work with GitHub Gists. See the release notes for changes. Checkout the docs to get started. vignette gains example of round-tripping a data.frame to a gist & back (@jsta); udpate docs regarding GitHub PAT;
gist_create()bug fix
v0.7.3) of DataSpaceR is on CRAN - interface to the CAVD DataSpace. See the release notes for changes. Checkout the docs to get started. v0.0.5) of plotdap is on CRAN - easily visualize data from ERDDAP servers via the rerddap package. See the release notes for changes. Checkout the vignette to get started. v0.5.0) of rdatacite is on CRAN - client for DataCite. See the release notes for changes. Checkout the README to get started. Major refactor to work with the new DataCite API: all functions from the previous version are defunct
v0.7.0) of rtweet is on CRAN - client for accessing Twitter’s REST and stream APIs. See the release notes for changes. Checkout the docs to get started. fixed numerous typos and grammatical mistakes; various bug fixes and stability improvements for data parsing
v1.0.0) of fingertipsR is on CRAN - Fingertips data for public health http://fingertips.phe.org.uk/. See the release notes for changes. Checkout the vignettes to get started. We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following packages were recently submitted:
The following packages recently went through our software-review process and have been approved:
Code of Conduct:
Software Review:
Jeroen Ooms wrote about Working with audio in R using av. av package: https://docs.ropensci.org/av/
![](\"../assets/img/av.png\")
The following 18 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
Maëlle Salmon asked a good question that’s gathering lots of input: How do you securely share credentials in your team?
Three use cases have been reported in the forum recently:
Kevin Zolea wrote a blog post on visualizing snowfall data using rnoaa: Making a plot of December snowfall data in NJ with R’s ggplot2 & rnoaa
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had six recent examples of maintainer transitions within rOpenSci:
We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.
Faltýnek Fric, Z., Rindoš, M., & Konvička, M. (2019). Phenology responses of temperate butterflies to latitude depend on ecological traits. Ecology Letters, 23(1), 172–180. https://doi.org/10.1111/ele.13419 ↩
Firmansyah, F. M., & Jones, J. J. (2019). Did the Black Panther Movie Make Blacks Blacker? Examining Black Racial Identity on Twitter Before and After the Black Panther Movie Release. Social Informatics, 66–78. https://doi.org/10.1007/978-3-030-34971-4_5 ↩
Mancinelli, G., Mali, S., & Belmonte, G. (2019). Species Richness and Taxonomic Distinctness of Zooplankton in Ponds and Small Lakes from Albania and North Macedonia: The Role of Bioclimatic Factors. Water, 11(11), 2384. https://doi.org/10.3390/w11112384 ↩
Sigsgaard, E. E., Torquato, F., Frøslev, T. G., Moore, A. B. M., Sørensen, J. M., Range, P., … Thomsen, P. F. (2019). Using vertebrate environmental DNA from seawater in biomonitoring of marine habitats. Conservation Biology. https://doi.org/10.1111/cobi.13437 ↩
Toussaint, A., Bueno, G., Davison, J., Moora, M., Tedersoo, L., Zobel, M., … Pärtel, M. (2019). Asymmetric patterns of global diversity among plants and mycorrhizal fungi. Journal of Vegetation Science. https://doi.org/10.1111/jvs.12837 ↩
Roddy, A. B., Théroux-Rancourt, G., Abbo, T., Benedetti, J. W., Brodersen, C. R., Castro, M., … Simonin, K. A. (2019). The Scaling of Genome Size and Cell Size Limits Maximum Rates of Photosynthesis with Implications for Ecological Strategies. International Journal of Plant Sciences. https://doi.org/10.1086/706186> ↩
Malaj, E., Liber, K., & Morrissey, C. A. (2019). Spatial distribution of agricultural pesticide use and predicted wetland exposure in the Canadian Prairie Pothole Region. Science of The Total Environment, 134765. https://doi.org/10.1016/j.scitotenv.2019.134765 ↩
Ulibarri, N., & Scott, T. A. (2019). Environmental hazards, rigid institutions, and transformative change: How drought affects the consideration of water and climate impacts in infrastructure management. Global Environmental Change, 59, 102005. https://doi.org/10.1016/j.gloenvcha.2019.102005 ↩
Espinosa, B. S., D’Apolito, C., Silva-Caminha, S. A. F., Ferreira, M. G., & Absy, M. L. (2020). Neogene paleoecology and biogeography of a Malvoid pollen in northwestern South America. Review of Palaeobotany and Palynology, 273, 104131. https://doi.org/10.1016/j.revpalbo.2019.104131 ↩
Upham, N. S., Esselstyn, J. A., & Jetz, W. (2019). Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLOS Biology, 17(12), e3000494. https://doi.org/10.1371/journal.pbio.3000494 ↩
Jin, J., & Yang, J. (2020). BDcleaner: A workflow for cleaning taxonomic and geographic errors in occurrence data archived in biodiversity databases. Global Ecology and Conservation, 21, e00852. https://doi.org/10.1016/j.gecco.2019.e00852 ↩
Stévart, T., Dauby, G., Lowry, P. P., Blach-Overgaard, A., Droissart, V., Harris, D. J., … Couvreur, T. L. P. (2019). A third of the tropical African flora is potentially threatened with extinction. Science Advances, 5(11), eaax9444. https://doi.org/10.1126/sciadv.aax9444 ↩
D’Amen, M., & Azzurro, E. (2019). Lessepsian fish invasion in Mediterranean marine protected areas: a risk assessment under climate change scenarios. ICES Journal of Marine Science, 77(1), 388–397. https://doi.org/10.1093/icesjms/fsz207 ↩
Zizka, A., Azevedo, J., Leme, E., Neves, B., Costa, A. F., Caceres, D., & Zizka, G. (2019). Biogeography and conservation status of the pineapple family (Bromeliaceae). Diversity and Distributions, 26(2), 183–195. https://doi.org/10.1111/ddi.13004 ↩
Knoploch, C., C. Grinand, G. Vieilledent. 2019. The importance of deforestation and climate change in shaping lemurs’ distributions and identifying their areas of climatic refuges. Thesis. http://bit.ly/2tmBx0u ↩
Badreldin, N., Abu Hatab, A., & Lagerkvist, C.-J. (2019). Spatiotemporal dynamics of urbanization and cropland in the Nile Delta of Egypt using machine learning and satellite big data: implications for sustainable development. Environmental Monitoring and Assessment, 191(12). https://doi.org/10.1007/s10661-019-7934-x ↩
Brown, E.E. 2019. Alzheimer’s Disease Pathophysiology and Risk Factors with Amyloid Positron Emission Tomography, an Open Science Approach, and the Consideration of Environmental Exposures. Master’s Thesis. https://tspace.library.utoronto.ca/bitstream/1807/97859/1/Brown_Eric_E_201911_MSc_thesis.pdf ↩
Booth, A., Bell, T., Halhol, S., Pan, S., Welch, V., Merinopoulou, E., … Cox, A. (2019). Using Social Media to Uncover Treatment Experiences and Decisions in Patients With Acute Myeloid Leukemia or Myelodysplastic Syndrome Who Are Ineligible for Intensive Chemotherapy: Patient-Centric Qualitative Data Analysis. Journal of Medical Internet Research, 21(11), e14285. https://doi.org/10.2196/14285 ↩
Do you Want to Intern with rOpenSci’s Community Manager?: Stefanie Butland. Details are in the blog post.
We want to thank everyone in the rOpenSci community who contributed code, issues, and otherwise over the last year: Thank You, 2019.
CRAN: GitHub:
v0.3.2) of phylocomr is on CRAN - Interface to Phylocom for analysis of phylogenetic community structure and character evolution. See the release notes for changes. Checkout the vignette to get started. bug fix for gcc -fno-common
v0.1.2) of osmdata is on CRAN - import OpenStreetMap data as simple features or spatial objects. See the release notes for changes. Checkout the docs to get started. new fxn
unname_osmdata_sf()to remove row names from sf objects; minor changes; bug fixes
v1.4.0) of fulltext is on CRAN - full text of scholarly articles across many data sources. See the release notes for changes. Checkout the fulltext book to get started.
ft_get()gains new publisher plugin (Cambridge); Wiley now has xml
v1.2.10) of UCSCXenaTools is on CRAN - download and explore datasets from UCSC Xena data hubs. See the release notes for changes. Checkout the docs to get started. updated newest dataset list of UCSC Xena hubs
v1.23) of rtika is on CRAN - R Interface to Apache Tika. See the release notes for changes. Checkout the docs to get started. updated Tika to 1.23
v1.0.5) of essurvey is on CRAN - data from the European Social Survey. See the release notes for changes. Checkout the docs to get started. dont run examples on cran
v0.2.2) of citecorp is on CRAN - client for the Open Citations Corpus. See the release notes for changes. Checkout the docs to get started. better check if Citecorp is up before running examples
We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
No new submissions or approved submissions.
It’s time for another installment of … 2 Months in 2 Minutes - rOpenSci News, December 2019 - if you want a brief summary of the last 2 months of these newsletters, these blog posts are for you (written by Stefanie Butland)
Scott Chamberlain wrote about HTTP testing in R: overview of tools and new features
Through time URLs can lead to nowhere, to sites that don’t exist anymore. We’ve accumulated many of these bad links in our website (https://ropensci.org/). Maëlle Salmon, Stefanie Butland, and Scott Chamberlain wrote about cleaning the bad links: We cleaned our website URLs with R!
The following 18 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had six recent examples of maintainer transitions within rOpenSci:
We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.
Gryseels, S., Watts, T. D., Kabongo, J.-M. M., Larsen, B. B., Lemey, P., Muyembe-Tamfum, J.-J., … Worobey, M. (2019). A near-full-length HIV-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue. https://doi.org/10.1101/687863 ↩
Wittouck, S., Wuyts, S., Meehan, C. J., van Noort, V., & Lebeer, S. (2019). A Genome-Based Species Taxonomy of the Lactobacillus Genus Complex. mSystems, 4(5). https://doi.org/10.1128/msystems.00264-19 ↩
O’Rourke, D. R. (2019). Molecular Diet Analyses of North American Bats (Doctoral dissertation, University of New Hampshire). https://search.proquest.com/openview/b4e35aa33ed9212841cf9cdb83b3448f/1 ↩
Hamdi, T., Slimi, H., Bounhas, I., & Slimani, Y. (2020, January). A Hybrid Approach for Fake News Detection in Twitter Based on User Features and Graph Embedding. In International Conference on Distributed Computing and Internet Technology (pp. 266-280). Springer, Cham. https://link.springer.com/chapter/10.1007/978-3-030-36987-3_17 ↩
Roh, T., Jeong, Y., Jang, H., & Yoon, B. (2019). Technology opportunity discovery by structuring user needs based on natural language processing and machine learning. PLOS ONE, 14(10), e0223404. https://doi.org/10.1371/journal.pone.0223404 ↩
Benun Sutton, F., & Wilson, A. B. (2019). Where are all the moms? External fertilization predicts the rise of male parental care in bony fishes. Evolution. https://doi.org/10.1111/evo.13846 ↩
Yang, D. (2019). Making reference solar forecasts with climatology, persistence, and their optimal convex combination. Solar Energy, 193, 981–985. https://doi.org/10.1016/j.solener.2019.10.006 ↩
Zheleznova, G., Shubina, T., Degteva, S., Chadin, I., & Rubtsov, M. (2019). Moss occurrences in Yugyd Va National Park, Subpolar and Northern Urals, European North-East Russia. Biodiversity Data Journal, 7. https://doi.org/10.3897/bdj.7.e32307 ↩
Kearney, M. R., Gillingham, P. K., Bramer, I., Duffy, J. P., & Maclean, I. M. D. (2019). A method for computing hourly, historical, terrain‐corrected microclimate anywhere on earth. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13330 ↩
Alex Dornburg, Dustin J. Wcisel, J. Thomas Howard et al. Transcriptome Ortholog Alignment Sequence Tools (TOAST) for Phylogenomic Dataset Assembly, 21 October 2019, PREPRINT (Version 1) available at Research Square https://doi.org/10.21203/rs.2.16269/v1 ↩
Elmslie, B. G., Gushulak, C. A., Boreux, M. P., Lamoureux, S. F., Leavitt, P. R., & Cumming, B. F. (2019). Complex responses of phototrophic communities to climate warming during the Holocene of northeastern Ontario, Canada. The Holocene, 095968361988301. https://doi.org/10.1177/0959683619883014 ↩
Rodewald, A. D., Strimas-Mackey, M., Schuster, R., & Arcese, P. (2019). Tradeoffs in the value of biodiversity feature and cost data in conservation prioritization. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-52241-2 ↩
Outhwaite, C. L., Powney, G. D., August, T. A., Chandler, R. E., Rorke, S., Pescott, O. L., … Isaac, N. J. B. (2019). Annual estimates of occupancy for bryophytes, lichens and invertebrates in the UK, 1970–2015. Scientific Data, 6(1). https://doi.org/10.1038/s41597-019-0269-1 ↩
Schwarz, M. 2019 Protecting the predators? Assessing the overlap between marine protected areas and endangered shark species on a global scale. http://bit.ly/2QDNbgS ↩
Smith, T. P., Thomas, T. J. H., García-Carreras, B., Sal, S., Yvon-Durocher, G., Bell, T., & Pawar, S. (2019). Community-level respiration of prokaryotic microbes may rise with global warming. Nature Communications, 10(1). https://doi.org/10.1038/s41467-019-13109-1 ↩
Özyıldırım, E. (2019). Subjective Value Assessment Based on Emojis for Applications in Landscape and Urban Planning (Doctoral dissertation, Department of Geo-information Processing, University of Twente). https://cartographymaster.eu/wp-content/theses/2019_Ozyildirim_Thesis.pdf ↩
Mpandeli, S., Nhamo, L., Moeletsi, M., Masupha, T., Magidi, J., Tshikolomo, K., … Mabhaudhi, T. (2019). Assessing climate change and adaptive capacity at local scale using observed and remotely sensed data. Weather and Climate Extremes, 26, 100240. https://doi.org/10.1016/j.wace.2019.100240 ↩
Ahmad, S., Yang, L., Khan, T. U., Wanghe, K., Li, M., & Luan, X. (2020). Using an ensemble modelling approach to predict the potential distribution of Himalayan gray goral (Naemorhedus goral bedfordi) in Pakistan. Global Ecology and Conservation, 21, e00845. https://doi.org/10.1016/j.gecco.2019.e00845 ↩
CRAN: GitHub:
v0.1.4) of baRcodeR after going through rOpenSci software review is on CRAN - the package deals with label creation for tracking and collecting data from biological samples. See the release notes for changes. Checkout the docs to get started. v2.0.1) of EML is on CRAN - read and write ecological metadata language files. See the release notes for changes. Checkout the docs to get started. improve error messages; pandoc fixes; improve docs
v0.2.21) of rglobi is on CRAN - R Interface to Global Biotic Interactions. See the release notes for changes. Checkout the vignette to get started. tests fixes
v0.5.0) of webmockr is on CRAN - stubbing and setting expectations on HTTP requests. See the release notes for changes. Checkout the HTTP testing book to get started. now supports writing to disk mocking & mocking simple auth with httr works now
v0.4.0) of vcr is on CRAN - record HTTP calls to disk for test caching. See the release notes for changes. Checkout the HTTP testing book to get started. now handles writing to disk; can now turn vcr completely off with a fxn call or env var; igoring specific requests now works; many httr fixes; much better docs for R6 classes
v0.2.7) of tradestatistics is on CRAN - open trade statistics api wrapper and utility program. See the release notes for changes. Checkout the docs to get started. v0.4.0) of nlrx is on CRAN - setup, run and analyze NetLogo model simulations. See the release notes for changes. Checkout the vignettes to get started. new vignette; new crayon and EasyABC pkg deps; pandoc added to sys reqs
v2.1.1) of beastier is on CRAN - Provides a way to call BEAST2 from R. See the release notes for changes. Checkout the docs to get started. gains a vignette
v2.0.5) of mauricer is on CRAN - install BEAST2 packages. See the release notes for changes. Checkout the docs to get started. gains a vignette
v2.0.2) of tracerer is on CRAN - parse and analyze BEAST2 input files programmatically. See the release notes for changes. Checkout the vignettes to get started. gains a vignette; better error checking
v2.3.2) of beautier is on CRAN - create BEAST2 input files programmatically. See the release notes for changes. Checkout the vignettes to get started. v7.8.0) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started. dynamic branching implemented; new fxns subtargets, get_trace/read_trace, id_chr; bug fixes and many improvements
v0.5.0) of tidyhydat is on CRAN - Water Survey of Canada hydrometric data. See the release notes for changes. Checkout the vignettes to get started. bug fixes; allow downloading HYDAT to altnerative location; better docs
v0.6.1) of epubr is on CRAN - read EPUB File Metadata and Text. See the release notes for changes. Checkout the docs to get started. fix warnings from a package dependency
v0.3.4) of eia is on CRAN - API wrapper for US Energy Information Administration open data. See the release notes for changes. Checkout the docs to get started. v1.2) of writexl is on CRAN - a portable, light-weight data frame to xlsx exporter. See the release notes for changes. Checkout the README to get started. update bundled libxlswriter to v0.8.8; xl_formula and xl_hyperlink now correctly support NA
v2.0.2) of skimr is on CRAN - compact and flexible summaries of data. See the release notes for changes. Checkout the vignettes to get started. v0.2.4) of tiler is on CRAN - generate geographic and non-geographic map tiles from R. See the release notes for changes. Checkout the docs to get started. now precompiling vignettes; update gdal2tiles to v2.4; updated docs
We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
No new submissions or approved submissions.
Jeroen Ooms wrote about How to precompute package vignettes or pkgdown articles.
The following 11 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had six recent examples of maintainer transitions within rOpenSci:
We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.
Paudyal, N., Pan, H., Elbediwi, M., Zhou, X., Peng, X., Li, X., … Yue, M. (2019). Characterization of Salmonella Dublin isolated from bovine and human hosts. BMC Microbiology, 19(1). https://doi.org/10.1186/s12866-019-1598-0 ↩
Bohner, T., & Diez, J. (2019). Extensive mismatches between species distributions and performance and their relationship to functional traits. Ecology Letters. https://doi.org/10.1111/ele.13396 ↩
Defolie, C., Merkling, T., & Fichtel, C. (2019). Patterns and variation in the mammal parasite–glucorticoid relationship. Biological Reviews. https://doi.org/10.1111/brv.12555 ↩
Blischak, J. D., Carbonetto, P., & Stephens, M. (2019). Creating and sharing reproducible research code the workflowr way. F1000Research, 8, 1749. https://doi.org/10.12688/f1000research.20843.1 ↩
Millard, J. W., Freeman, R., & Newbold, T. (2019). Text‐analysis reveals taxonomic and geographic disparities in animal pollination literature. Ecography. https://doi.org/10.1111/ecog.04532 ↩
Hung, T., Rosales, M., Kurobe, T., Stevenson, T., Ellison, L., Tigan, G., … Teh, S. (2019). A pilot study of the performance of captive‐reared delta smelt Hypomesus transpacificus in a semi‐natural environment. Journal of Fish Biology. https://doi.org/10.1111/jfb.14162 ↩
Chalmandrier, L., Pansu, J., Zinger, L., Boyer, F., Coissac, E., Génin, A., … Thuiller, W. (2019). Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales. Ecography. https://doi.org/10.1111/ecog.04492 ↩
Mishra, P., & Narayan Tripathi, L. (2019). Characterization of two‐dimensional materials from Raman spectral data. Journal of Raman Spectroscopy. https://doi.org/10.1002/jrs.5744 ↩
Christensen, A. P., & Kenett, Y. (2019, October 22). Semantic Network Analysis (SemNA): A Tutorial on Preprocessing, Estimating, and Analyzing Semantic Networks. https://doi.org/10.31234/osf.io/eht87 ↩
Zhong, B. H. W., Wiersma, J. J., Sheaffer, C. C., Steffenson, B. J., & Smith, K. P. (2019). Assessment of Winter Barley in Minnesota: Relationships among Cultivar, Fall Seeding Date, Winter Survival, and Grain Yield. Cftm, 5(1), 0. https://doi.org/10.2134/cftm2019.07.0055 ↩
Tada, I., Tsugawa, H., Meister, I., Zhang, P., Shu, R., Katsumi, R., … Chaleckis, R. (2019). Creating a Reliable Mass Spectral–Retention Time Library for All Ion Fragmentation-Based Metabolomics. Metabolites, 9(11), 251. https://doi.org/10.3390/metabo9110251 ↩
CRAN: GitHub:
v0.1) of lightr is on CRAN - read spectrometric data and metadata. Checkout the docs to get started. v2.0.3) of mauricer is on CRAN - install BEAST2 packages. Checkout the docs to get started. v0.3.0) of phylocomr is on CRAN - Interface to Phylocom for analysis of phylogenetic community structure and character evolution. See the release notes for changes. Checkout the vignette to get started. now always use temp files even when users pass files to avoid altering user files; new manual file describing inputs; check taxon name case in all inputs
v1.2.9) of UCSCXenaTools is on CRAN - download and explore datasets from UCSC Xena data hubs. See the release notes for changes. Checkout the docs to get started. v0.4.12) of iheatmapr is on CRAN - Interactive and complex heatmaps. See the release notes for changes. Checkout the docs to get started. adjust tests to be compatible with newer version of scales package
v0.4.1) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. better error messages if
od2line()fails due to non-matching ids; improved documentation ofod2line()in the vignette
v1.0.15) of lingtypology is on CRAN - linguistic typology and mapping. See the release notes for changes. Checkout the docs to get started. remove
NAapearence from popup window when “fake” language argument is used; fast fix of colors tests
v0.2.3) of tiler is on CRAN - generate geographic and non-geographic map tiles from R. See the release notes for changes. Checkout the docs to get started. precompile vignette that depends on external data
v2.0) of skimr is on CRAN - compact and flexible summaries of data. See the release notes for changes. Checkout the vignettes to get started. a complete re-write! check out the release notes for all the details 🎉
v0.9.5) of rnoaa is on CRAN - NOAA Weather Data from R. See the release notes for changes. Checkout the vignettes to get started.
lcd()base url fixed (please upgrade if you use lcd data); allgefsfunctions temporarily defunct
v0.2.0) of git2rdata is on CRAN - store and retrieve data.frames in a Git repository. See the release notes for changes. Checkout the docs to get started. a number of breaking changes, and some new features
v1.1.3) of nasapower is on CRAN - NASA POWER API Client. See the release notes for changes. Checkout the docs to get started. new vignette “Using nasapower with large geographic areas”
v0.9.91) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started.
get_idscan now suppress package cli messages; many improvements and bug fixes; force HTTP/1.1 for NCBI; warn when taxon identifiers of class X don’t matchdbparam value; beware: COL now rate limits
v0.4.0) of nodbi is on CRAN - the NoSQL database connector. See the release notes for changes. Checkout the README to get started. in
docdb_query()anddocdb_get()for sqlite use a connection instead of file path; fix todocdb_query()anddocdb_create()for sqlite when handling mixed value types
We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following package recently went through our software review process and has been approved:
Nicholas Potter wrote about his recently approved package rnassqs for accessing USDA agricultural data: rnassqs: accessing USDA agricultural data via API
![](\"../assets/img/rnassqs.png\")
Vikram Baliga wrote about his recently approved package workloopR - Analysis of work loops and other data from muscle physiology experiments in R
![](\"../assets/img/workloopR_icon_300dpi.png\"){kind=icon}
The following 12 works use/cite rOpenSci software:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had six recent examples of maintainer transitions within rOpenSci:
We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.
Fecchio, A., Bell, J. A., Bosholn, M., Vaughan, J. A., Tkach, V. V., Lutz, H. L., … Clark, N. J. (2019). An inverse latitudinal gradient in infection probability and phylogenetic diversity for Leucocytozoon blood parasites in New World birds. Journal of Animal Ecology. https://doi.org/10.1111/1365-2656.13117 ↩
Scheffers, B. R., Oliveira, B. F., Lamb, I., & Edwards, D. P. (2019). Global wildlife trade across the tree of life. Science, 366(6461), 71–76. https://doi.org/10.1126/science.aav5327 ↩
Enkybayar, A., Haustein, S., Barata, G., & Alperin, J. P. Comparing public and private Facebook activity linking to PLOS ONE papers. Altmetrics 2019 Conference Proceedings http://altmetrics.org/wp-content/uploads/2019/10/Enkybayar_altmetrics19_paper_8.pdf ↩
Lewinski, D., & Hasan, M. R. Russian Troll Account Classification with Twitter and Facebook Data. http://bit.ly/2smxrVz ↩
Dumitrescu, A., Cheval, S., & Guijarro, J. A. (2019). Homogenization of a combined hourly air temperature dataset over Romania. International Journal of Climatology. https://doi.org/10.1002/joc.6353 ↩
Yoo, B. H., Kim, K. S., & Lee, J. (2019). The use of MODIS atmospheric products to estimate cooling degree days at weather stations in South and North Korea. Korean Journal of Agricultural and Forest Meteorology, 21(2), 97-109. https://doi.org/10.5532/KJAFM.2019.21.2.97 ↩
Kaaronen, R. O., & Strelkovskii, N. (2019). Cultural Evolution of Sustainable Behaviours: Pro-Environmental Tipping Points in an Agent-Based Model. https://doi.org/10.31234/osf.io/w6dpa ↩
Sydenham, M. A. K., Moe, S. R., & Eldegard, K. (2020). When context matters: Spatial prediction models of environmental conditions can identify target areas for wild bee habitat management interventions. Landscape and Urban Planning, 193, 103673. https://doi.org/10.1016/j.landurbplan.2019.103673 ↩
Bottin, M., Peyre, G., Vargas, C., Raz, L., Richardson, J. E., & Sanchez, A. (2019). Phytosociological data and herbarium collections show congruent large scale patterns but differ in their local descriptions of community composition. Journal of Vegetation Science. https://doi.org/10.1111/jvs.12825 ↩
Piatscheck, F. (2019). Past, present and future: Geographic and temporal variation in a Fig–fig wasp mutualism (Order No. 22588967). ProQuest Dissertations & Theses Global. (2302689695). https://search.proquest.com/docview/2302689695 ↩
Reyes, A. L. P., Silva, T. C., Coetzee, S. G., Plummer, J. T., Davis, B. D., Chen, S., … Jones, M. R. (2019). GENAVi: a shiny web application for gene expression normalization, analysis and visualization. BMC Genomics, 20(1). https://doi.org/10.1186/s12864-019-6073-7 ↩
Fetter, K.C. 2019. Natural Selection For Disease Resistance In Hybrid Poplars Targets Stomatal Patterning Traits And Regulatory Genes. Graduate College Dissertations and Theses. 1162. https://scholarworks.uvm.edu/graddis/1162 ↩
rOpenSci Announces a New $896k Award From The Gordon and Betty Moore Foundation to Improve the Scientific Package Ecosystem for R. Read the blog post by Karthik Ram
CRAN: GitHub:
v2.3) of pdftools is on CRAN - Text extraction, rendering and converting of PDF documents. See the release notes for changes. Checkout the README to get started. pdf_text() improvements; new fxns pdf_ocr_text/pdf_ocr_data wrap tesseract
v0.5.3) of gender is on CRAN - Predict gender from names using historical data. See the release notes for changes. Checkout the vignette to get started. docs improvements, testing fixes
v2.4.0) of RNeXML is on CRAN - Semantically Rich I/O for the NeXML Format. See the release notes for changes. Checkout the vignettes to get started. use Additional_repositories for taxadb
v0.2.0) of citecorp is on CRAN - client for the Open Citations Corpus. See the release notes for changes. Checkout the docs to get started. oc_doi2ids/oc_pmid2ids/oc_pmcid2ids functions now vectorized; bug fixes
v0.9.4) of rnoaa is on CRAN - NOAA Weather Data from R. See the release notes for changes. Checkout the vignettes to get started. new gefs fxns gefs_dimensions/gefs_ensembles; gefs fxn fixes; argo family fxns no longer work as API is gone - but FTP fxns still work (
argo_guoy_files()/argo())
v0.2.3) of tidync is on CRAN - a tidy approach to NetCDF data exploration and extraction. See the release notes for changes. Checkout the docs to get started. test fixes
v0.9.0) of crul is on CRAN - an R6 based HTTP client for R made for developers. See the release notes for changes. Checkout the docs to get started. HttpResponse object gains methods for checking response content type; head verb now uses auth correctly
v1.0.4) of essurvey is on CRAN - data from the European Social Survey. See the release notes for changes. Checkout the docs to get started. v1.1.4) of solrium is on CRAN - general purpose R interface to Solr. See the release notes for changes. Checkout the vignettes to get started. fix
delete_by_query()/$delete_by_query()method
v1.0.2) of spocc is on CRAN - an interface to many species occurrence data sources. See the release notes for changes. Checkout the docs to get started. fix failing tests on cran
v1.4.0) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the occurrence manual to get started. new fxn
mvt_fetch()for GBIF’s Map Vector Tiles; overhaul ofocc_issues/name_issuesfxns; many fixes
v0.8.0) of geojsonio is on CRAN - Convert Data from and to GeoJSON or TopoJSON. See the release notes for changes. Checkout the vignettes to get started.
geojson_read()gains method for PostGIS;geojson_read()now uses sf instead of sp;geojson_list()gains precision param; bug fixes
v0.8.0) of ritis is on CRAN - an R client for ITIS (Integrated Taxonomic Information Service). See the release notes for changes. Checkout the docs to get started. improve
itis_search()examples; bug fix foritis_group()
We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following package was recently submitted:
The following packages recently went through our software review process and have been approved:
Michael Quinn and Elin Waring wrote about a new version (v2) of their package skimr - (Re)introducing skimr v2 - A year in the life of an open source R project
![](\"../assets/img/skimr_logo.png\"){kind=logo}
Michael Sumner wrote about his package tidync that was recently approved in rOpenSci software review - tidync: scientific array data from NetCDF in R
![](\"../assets/img/oisst-data-single-line-1.png\")
The following 15 works use/cite rOpenSci software:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had six recent examples of maintainer transitions within rOpenSci:
We’ve got one package in need of a new maintainer:
Palstrøm N.B., Matthiesen R., Beck H.C. (2020) Data Imputation in Merged Isobaric Labeling-Based Relative Quantification Datasets. In: Matthiesen R. (eds) Mass Spectrometry Data Analysis in Proteomics. Methods in Molecular Biology, vol 2051. Humana, New York, NY https://doi.org/10.1007/978-1-4939-9744-2_13 ↩
Cinelli, M., Ficcadenti, V., & Riccioni, J. (2019). The interconnectedness of the economic content in the speeches of the US Presidents. Annals of Operations Research. https://doi.org/10.1007/s10479-019-03372-2 ↩
Umlauf, N., Klein, N., Simon, T., & Zeileis, A. (2019). bamlss: A Lego Toolbox for Flexible Bayesian Regression (and Beyond). arXiv preprint arXiv:1909.11784. https://arxiv.org/abs/1909.11784 ↩
Bager Olsen, M. T., Geldmann, J., Harfoot, M., Tittensor, D. P., Price, B., Sinovas, P., … Burgess, N. D. (2019). Thirty-six years of legal and illegal wildlife trade entering the USA. Oryx, 1–10. https://doi.org/10.1017/s0030605319000541 ↩
Vidal, M. C., Quinn, T. W., Stireman, J. O., Tinghitella, R. M., & Murphy, S. M. (2019). Geography is more important than host plant use for the population genetic structure of a generalist insect herbivore. Molecular Ecology. https://doi.org/10.1111/mec.15218 ↩
De Luca, D., Kooistra, W. H. C. F., Sarno, D., Gaonkar, C. C., & Piredda, R. (2019). Global distribution and diversity of Chaetoceros (Bacillariophyta, Mediophyceae): integration of classical and novel strategies. PeerJ, 7, e7410. https://doi.org/10.7717/peerj.7410 ↩
Ondra, M. 2019. Reliability based design approach to stochastic supply planning. https://iaee2019ljubljana.oyco.eu/download/contribution/fullpaper/345/345_fullpaper_20190608_130510.pdf ↩
Wang, Y., Goring, S. J., & McGuire, J. L. (2019). Bayesian ages for pollen records since the last glaciation in North America. Scientific Data, 6(1). https://doi.org/10.1038/s41597-019-0182-7 ↩
Nalborczyk, L., Grandchamp, R., Koster, E. H. W., Perrone-Bertolotti, M., & Loevenbruck, H. (2019). Can we decode phonetic features in inner speech using surface electromyography? https://doi.org/10.31234/osf.io/8v5yd ↩
Stanstrup, J., Broeckling, C., Helmus, R., Hoffmann, N., Mathé, E., Naake, T., … Neumann, S. (2019). The metaRbolomics Toolbox in Bioconductor and beyond. Metabolites, 9(10), 200. https://doi.org/10.3390/metabo9100200 ↩
Feng, X., Park, D. S., Walker, C., Peterson, A. T., Merow, C., & Papeş, M. (2019). A checklist for maximizing reproducibility of ecological niche models. Nature Ecology & Evolution. https://doi.org/10.1038/s41559-019-0972-5 ↩
Duffany, J. (2019). Developing CyberSecurity Skills with Intermediate Programming Courses. Proceedings of the 17th LACCEI International Multi-Conference for Engineering, Education, and Technology: “Industry, Innovation, and Infrastructure for Sustainable Cities and Communities.” https://doi.org/10.18687/laccei2019.1.1.414 ↩
Maherali, H. (2019). Mutualism as a plant functional trait: linking variation in the mycorrhizal symbiosis to climatic tolerance, geographic range and population dynamics. International Journal of Plant Sciences. https://doi.org/10.1086/706187 ↩
Havinga, I., Hein, L., Vega-Araya, M., & Languillaume, A. (2020). Spatial quantification to examine the effectiveness of payments for ecosystem services: A case study of Costa Rica’s Pago de Servicios Ambientales. Ecological Indicators, 108, 105766. https://doi.org/10.1016/j.ecolind.2019.105766 ↩
Jin, L., Tefft, B. C., & Horrey, W. J. (2019). Mining consumer complaints to identify unsuccessful interactions with advanced driver assistance systems. Proceedings of the 11th International Conference on Automotive User Interfaces and Interactive Vehicular Applications Adjunct Proceedings - AutomotiveUI ’19. https://doi.org/10.1145/3349263.3351313 ↩
CRAN: GitHub:
v2.0.4) of ijtiff is on CRAN - Comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started. link to docs in DESCRIPTION file; fix for
pkg-config
v1.1.0) of rebird is on CRAN - client for the eBird database of bird observations. See the release notes for changes. Checkout the vignette to get started. updated internal taxonomy; new fxn
ebirdhistoricalwith historical observations
v0.9.2) of rnoaa is on CRAN - NOAA Weather Data from R. See the release notes for changes. Checkout the vignettes to get started.
gefs()gains new parametersens/timereplacingens_idx/time_idx;isd()now fetches data via http rather than ftp;tornadoes()fix
v1.0.0) of spocc is on CRAN - an interface to many species occurrence data sources. See the release notes for changes. Checkout the docs to get started. source inat can now return photo metadata; docs improvements; bug fixes
v0.2.2) of tidync is on CRAN - a tidy approach to NetCDF data exploration and extraction. See the release notes for changes. Checkout the docs to get started. test fix
v1.1.0) of solrium is on CRAN - general purpose R interface to Solr. See the release notes for changes. Checkout the vignettes to get started. docs fixes; group queries fixed (were failing due to a parsing error)
v0.9.9) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started. EUBON fxns using their new API;
synonyms()returned data more consistent now; fix XML parsing for COL; datasets in onLoad so available in fxn calls w/o pkg loaded;sci2comm/comm2sciwithdb=\"ncbi\"no longer stop on no match found; many bug fixes
v1.3.2) of datapack is on CRAN - flexible container to transport and manipulate data. See the release notes for changes. Checkout the docs to get started. ensure that a ‘dc:creator’/’dcterms:modified’ elements are always present; gains fxn
removeRelationships(); remove dependency onredland::getNextResult
v7.7.0) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started. bug fix (use sum instead of max in
dir_size()); gains fxnswhich_clean(),drake_tempfile(), andcode_to_function()
v1.0.3) of essurvey is on CRAN - data from the European Social Survey. See the release notes for changes. Checkout the docs to get started. breaking changes (see news); you can now download SDDF (weight data) for each country/round combination of files; new package website https://docs.ropensci.org/essurvey
v0.0.4) of plotdap is on CRAN - easily visualize data from ERDDAP servers via the rerddap package. See the release notes for changes. Checkout the vignette to get started. minor fixes
v1.1.0) of stats19 is on CRAN - Work with Open Road Traffic Casualty Data from Great Britain. See the release notes for changes. Checkout the docs to get started. can now download 2018 data; bug fixes; new vignette
We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following package recently went through our software-review process and has been approved:
It’s time for another installment of … 2 Months in 2 Minutes - rOpenSci News, October 2019 - if you want a brief summary of the last 2 months of these newsletters, these blog posts are for you (written by Stefanie Butland)
Kevin Cazelles and Steve Vissault wrote about their recently approved package rmangal, an R client for the Mangal ecological interactions database - rmangal: making ecological networks easily accessible
![](\"../assets/img/rmangal.png\")
The following 13 works use/cite rOpenSci software:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had six recent examples of maintainer transitions within rOpenSci:
We’ve got one package in need of a new maintainer:
Friedman, M., Feilich, K. L., Beckett, H. T., Alfaro, M. E., Faircloth, B. C., Černý, D., … Harrington, R. C. (2019). A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean. Proceedings of the Royal Society B: Biological Sciences, 286(1910), 20191502. https://doi.org/10.1098/rspb.2019.1502 ↩
Sánchez-Tójar, A., Moran, N. P., O’Dea, R. E., Reinhold, K., & Nakagawa, S. (2019). Illustrating the importance of meta-analysing variances alongside means in ecology and evolution. https://doi.org/10.32942/osf.io/yhfvk ↩
Soh, P. X. Y., Marin Cely, J. M., Mortlock, S.-A., Jara, C. J., Booth, R., Natera, S., … Williamson, P. (2019). Genome-wide association studies of 74 plasma metabolites of German shepherd dogs reveal two metabolites associated with genes encoding their enzymes. Metabolomics, 15(9). https://doi.org/10.1007/s11306-019-1586-2 ↩
Li, X., Zhu, H., Geisen, S., Bellard, C., Hu, F., Li, H., … Liu, M. (2019). Agriculture erases climate constraints on soil nematode communities across large spatial scales. Global Change Biology. https://doi.org/10.1111/gcb.14821 ↩
Hwang, L. J., Pauloo, R. A., & Carlen, J. (2019). Assessing Impact of Outreach through Software Citation for Community Software in Geodynamics. Computing in Science & Engineering, 1–1. https://doi.org/10.1109/mcse.2019.2940221 ↩
Dick, E.J. and He, X. 2019. Status of Cowcod (Sebastes levis) in 2019. Pacific Fishery Management Council, Portland, OR. https://www.pcouncil.org/wp-content/uploads/2019/08/H5_Att9_Cowcod_2019_Full_E-Only_SEPT2019BB.pdf ↩
Flower, C. (2019). Food Plant Biogeography of the Sonoran Desert (Doctoral dissertation, Arizona State University). https://search.proquest.com/docview/2275500833 ↩
Enkhbayar, A., Haustein, S., Barata, G., & Alperin, J. P. (2019). How much research shared on Facebook is hidden from public view? A comparison of public and private online activity around PLOS ONE papers. arXiv preprint arXiv:1909.01476. https://arxiv.org/abs/1909.01476 ↩
Singh, J. 2019. Modelling Forest Lake Water Quality and Ecosystem Dynamics. Undergraduate Thesis. https://www.brisbane.qld.gov.au/sites/default/files/20190820%20Forest%20Lake%20Appendix%20A.pdf ↩
Etherington, T., & Omondiagbe, O. (2019). virtualNicheR: generating virtual fundamental and realised niches for use in virtual ecology experiments. Journal of Open Source Software, 4(41), 1661. https://doi.org/10.21105/joss.01661 ↩
Cazelles, K., Bartley, T., Guzzo, M. M., Brice, M., MacDougall, A. S., Bennett, J. R., … McCann, K. S. (2019). Homogenization of freshwater lakes: recent compositional shifts in fish communities are explained by gamefish movement and not climate change. Global Change Biology. https://doi.org/10.1111/gcb.14829 ↩
Verstraeten, W. W., Dujardin, S., Hoebeke, L., Bruffaerts, N., Kouznetsov, R., Dendoncker, N., … Delcloo, A. W. (2019). Spatio-temporal monitoring and modelling of birch pollen levels in Belgium. Aerobiologia. https://doi.org/10.1007/s10453-019-09607-w ↩
Bufford, J. L., Hulme, P. E., Sikes, B. A., Cooper, J. A., Johnston, P. R., & Duncan, R. P. (2019). Novel interactions between alien pathogens and native plants increase plant‐pathogen network connectance and decrease specialization. Journal of Ecology. https://doi.org/10.1111/1365-2745.13293 ↩
CRAN: GitHub:
v0.1.2) of chlorpromazineR is on CRAN - convert antipsychotic doses to chlorpromazine equivalents. Checkout the docs to get started. This package recently went through rOpenSci software review. v2.0.0) of rmangal is on CRAN - interface to the Mangal database of ecological networks. Checkout the docs to get started. This package recently went through rOpenSci software review. v0.4.0) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. family of new fxns for adding new nodes to routes, route networks and sfNetwork objects; other new fxns
v0.4.0) of ckanr is on CRAN - R client for the CKAN API. See the release notes for changes. Checkout the docs to get started. ^^ improvements to ckan_fetch fxn (thanks Sharla Gelfand)
v0.3.0) of emld is on CRAN - ecological metadata as linked data. See the release notes for changes. Checkout the vignette to get started. now supports EML v2.2; fixed xml parsing issue; eml_validate change
v1.2.7) of UCSCXenaTools is on CRAN - download and explore datasets from UCSC Xena data hubs. See the release notes for changes. Checkout the docs to get started. vignette updated; new datasets added; bug fixes
v1.4.2) of MtreeRing is on CRAN - a shiny application for automatic measurements of tree-ring widths on digital images. See the release notes for changes. Checkout the docs to get started. Update GitHub links in ring_app_launch function
We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following package was recently submitted:
There’s a new version of the rOpenSci Dev Guide out. The software review editors wrote up a post describing the accumulated changes since v0.2: rOpenSci Dev Guide 0.3.0: Updates. Some highlights:
Scott Chamberlain wrote a post on updates to the cran checks API. The API now has a route to get CRAN check results by maintainer, badges for CRAN checks with a number of different scenarios, and gives access to recent (30 day), and older (back to December 2018) checks data.
The following 18 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had six recent examples of maintainer transitions within rOpenSci:
We’ve got one package in need of a new maintainer:
Ayodele Benjamin, E., Vincent, E., Claudius, A., Olatomiwa, L., & Dickson, E. (2019). Data-based investigation on the performance of an independent Gas turbine for electricity generation using real power measurements and other closely related parameters. Data in Brief, 104444. https://doi.org/10.1016/j.dib.2019.104444 ↩
Mendes, G., Paiva, J. G. S., & Schwartz, W. R. (2019, July). Point-Placement Techniques and Temporal Self-Similarity Maps for Visual Analysis of Surveillance Videos. In 2019 23rd International Conference Information Visualisation (IV) (pp. 127-132). IEEE. https://ieeexplore.ieee.org/iel7/8798596/8811888/08811966.pdf ↩
Stewart, D. B., Wright, J. R., Fowler, M., McLimans, C. J., Tokarev, V., Amaniera, I., … Lamendella, R. (2019). Integrated Meta-omics Reveals a Fungus-Associated Bacteriome and Distinct Functional Pathways in Clostridioides difficile Infection. mSphere, 4(4). https://doi.org/10.1128/msphere.00454-19 ↩
Lewis, M. J., Barnes, M. R., Blighe, K., Goldmann, K., Rana, S., Hackney, J. A., … Pitzalis, C. (2019). Molecular Portraits of Early Rheumatoid Arthritis Identify Clinical and Treatment Response Phenotypes. Cell Reports, 28(9), 2455–2470.e5. https://doi.org/10.1016/j.celrep.2019.07.091 ↩
Esperon‐Rodriguez, M., Power, S. A., Tjoelker, M. G., Beaumont, L. J., Burley, H., Caballero‐Rodriguez, D., & Rymer, P. D. (2019). Assessing the vulnerability of Australia’s urban forests to climate extremes. Plants, People, Planet. https://doi.org/10.1002/ppp3.10064 ↩
Lacy, S. N., Corcoran, D., Alò, D., Lessmann, J., Meza, F., & Marquet, P. A. (2019). Main drivers of freshwater fish diversity across extra-tropical Southern Hemisphere rivers. Hydrobiologia. https://doi.org/10.1007/s10750-019-04044-9 ↩
Gonçalves, B., Coutinho, D., Exel, J., Travassos, B., Lago, C., & Sampaio, J. (2019). Extracting spatial-temporal features that describe a team match demands when considering the effects of the quality of opposition in elite football. PLOS ONE, 14(8), e0221368. https://doi.org/10.1371/journal.pone.0221368 ↩
Urquhart-Cronish, M., & Otto, S. P. (2019). Gender and language use in scientific grant writing. FACETS, 4(1), 442–458. https://doi.org/10.1139/facets-2018-0039 ↩
Wegrzyn, J. L., Falk, T., Grau, E., Buehler, S., Ramnath, R., & Herndon, N. (2019). Cyberinfrastructure and resources to enable an integrative approach to studying forest trees. Evolutionary Applications. https://doi.org/10.1111/eva.12860 ↩
Redmond, M. D., Morris, T. L., & Cramer, M. C. (2019). The cost of standing tall: wood nutrients associated with tree invasions in nutrient‐poor fynbos soils of South Africa. Ecosphere, 10(9). https://doi.org/10.1002/ecs2.2831 ↩
Hanna, A., & Hanna, L.-A. (2019). Topic Analysis of UK Fitness to Practise Cases: What Lessons Can Be Learnt? Pharmacy, 7(3), 130. https://doi.org/10.3390/pharmacy7030130 ↩
Ramagopalan, S. V., Malcolm, B., Merinopoulou, E., McDonald, L., & Cox, A. (2019). Automated extraction of treatment patterns from social media posts: an exploratory analysis in renal cell carcinoma. Future Oncology. https://doi.org/10.2217/fon-2019-0406 ↩
Bayley, D. T. I., Mogg, A. O. M., Purvis, A., & Koldewey, H. J. (2019). Evaluating the efficacy of small‐scale marine protected areas for preserving reef health: A case study applying emerging monitoring technology. Aquatic Conservation: Marine and Freshwater Ecosystems. https://doi.org/10.1002/aqc.3215 ↩
Mihalitsis, M., & Bellwood, D. (2019). Functional implications of dentition-based morphotypes in piscivorous fishes. Royal Society Open Science, 6(9), 190040. https://doi.org/10.1098/rsos.190040 ↩
Greco, M., Jonkers, L., Kretschmer, K., Bijma, J., & Kucera, M. (2019). Depth habitat of the planktonic foraminifera Neogloboquadrina pachyderma in the northern high latitudes explained by sea-ice and chlorophyll concentrations. Biogeosciences, 16(17), 3425–3437. https://doi.org/10.5194/bg-16-3425-2019 ↩
Flower, C. (2019). Food Plant Biogeography of the Sonoran Desert (Doctoral dissertation, Arizona State University). https://search.proquest.com/docview/2275500833 ↩
Rebolj, M., Parmar, D., Maroni, R., Blyuss, O., & Duffy, S. W. (In press). Concurrent participation in screening for cervical, breast, and bowel cancer in England. Journal of Medical Screening. ↩
Sun, Z., Cang, J., Ruan, Y., & Zhu, D. (2019). Reporting gaps between news media and scientific papers on outdoor air pollution–related health outcomes: A content analysis. The International Journal of Health Planning and Management. https://doi.org/10.1002/hpm.2894 ↩
![](\"../assets/img/helpwanted.png\")
CRAN: GitHub:
v0.3.1) of weathercan is on CRAN - Download weather data from the Environment and Climate Change Canada website. See the release notes for changes. Checkout the docs to get started. internal changes only
v3.0.10) of rotl is on CRAN - an interface to the Open Tree of Life API. See the release notes for changes. Checkout the vignettes to get started. internal changes & updated docs
v0.3.0) of nlrx is on CRAN - setup, run and analyze NetLogo model simulations. See the release notes for changes. Checkout the vignettes to get started. updated docs; two new vignettes; changes to
simdesign_GenAlg,simdesign_GenSA,simdesign_simple, anddownload_netLogo
v0.9.0) of rnoaa is on CRAN - NOAA Weather Data from R. See the release notes for changes. Checkout the vignettes to get started. sea ice updates; new fxn
lcd_cleanup; docs updates; many 🐞 fixes
v0.2.9) of fingertipsR is on CRAN - Fingertips data for public health http://fingertips.phe.org.uk/. See the release notes for changes. Checkout the vignettes to get started. fixed firewall issue
v0.4.0) of auk is on CRAN - eBird data extraction and processing. See the release notes for changes. Checkout the docs to get started. updated to 2019 eBird taxonomy;
auk_observer()filter added
v1.4.1) of MtreeRing is on CRAN - a shiny application for automatic measurements of tree-ring widths on digital images. See the release notes for changes. Checkout the docs to get started. v3.1.1) of qualtRics is on CRAN - download Qualtrics survey data. See the release notes for changes. Checkout the docs to get started. fix bug in
infer_data_types(); improve docs; deprecateregisterOptions(); make data import more robust
v0.2.20) of rglobi is on CRAN - R Interface to Global Biotic Interactions. See the release notes for changes. Checkout the vignette to get started. use
readrpkg to avoid encoding issues on windows
v0.2.5) of tradestatistics is on CRAN - open trade statistics api wrapper and utility program. See the release notes for changes. Checkout the docs to get started. now requires R>=3.5; changes in
ots_create_tidy_data()
v0.3.0) of nodbi is on CRAN - the NoSQL database connector. See the release notes for changes. Checkout the README to get started. new author Ralf Herold contributed SQLite/json1 integration for all pkg methods;
docdb_updategains MongoDB method;etcdintegration dropped
v0.3.1) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. new logo;
line_to_points()deprecated ->od2line();line2pointsn()now works with sf objects; docs fixes
The staff supported package etseed is now archived on CRAN. It was an R client for the key-value store etcd. After understanding the etcd product more, we decided it’s not something R users are reaching for.
We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following package was recently submitted:
Scott Chamberlain wrote a post on his new package, citecorp: citecorp: working with open citations. citecorp brings R user’s data from the OpenCitations Corpus; check it out if you are looking for citation data for any reason.
Jeroen Ooms dug into image suite packages in a recent blog post: Updates to the rOpenSci image suite: magick, tesseract, and av. To learn more about these and other rOpenSci packages, check out articles on https://docs.ropensci.org.
The following 23 works use/cite rOpenSci software:
rdryad will be coming soon.We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had six recent examples of maintainer transitions within rOpenSci:
We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.
Atickem, A., Stenseth, N. C., Fashing, P. J., Nguyen, N., Chapman, C. A., Bekele, A., … Kalbitzer, U. (2019). Build science in Africa. Nature, 570(7761), 297–300. https://doi.org/10.1038/d41586-019-01885-1 ↩
Collins, R. A., Bakker, J., Wangensteen, O. S., Soto, A. Z., Corrigan, L., Sims, D. W., … Mariani, S. (2019). Non‐specific amplification compromises environmental DNA metabarcoding with COI. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13276 ↩
Van der Veer, C., Bruisten, S. M., van Houdt, R., Matser, A. A., Tachedjian, G., van de Wijgert, J. H. H. M., … van der Helm, J. J. (2019). Effects of an over-the-counter lactic-acid containing intra-vaginal douching product on the vaginal microbiota. BMC Microbiology, 19(1). https://doi.org/10.1186/s12866-019-1545-0 ↩
Petersen, A. H., & Ekstrøm, C. T. (2019). dataMaid: Your Assistant for Documenting Supervised Data Quality Screening in R. Journal of Statistical Software, 90(6). https://doi.org/10.18637/jss.v090.i06 ↩
Watson, O. J., Sumner, K. M., Janko, M., Goel, V., Winskill, P., Slater, H. C., … Parr, J. B. (2019). False-negative malaria rapid diagnostic test results and their impact on community-based malaria surveys in sub-Saharan Africa. BMJ Global Health, 4(4), e001582. https://doi.org/10.1136/bmjgh-2019-001582 ↩
Piper, A. M., Batovska, J., Cogan, N. O. I., Weiss, J., Cunningham, J. P., Rodoni, B. C., & Blacket, M. J. (2019). Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance. GigaScience, 8(8). https://doi.org/10.1093/gigascience/giz092 ↩
Macip Sancho, G. 2019. Deciphering host-pathogen interactions at the biomembrane interface, key to target therapeutical approaches against Mycoplasma genitalium. Masters Thesis. Universitat Oberta de Catalunya. http://hdl.handle.net/10609/97806 ↩
Sobreiro, J. F. F. 2019. Vegetation multitemporal responses to hydroclimate variations in the Espinhaço Range (Brazil). Masters Thesis. (link broken: http://hdl.handle.net/11449/183096) ↩
Brionne, A., Juanchich, A., & Hennequet-Antier, C. (2019). ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity. BioData Mining, 12(1). https://doi.org/10.1186/s13040-019-0204-1 ↩
Fernandez-Basso, C., Ruiz, M. D., Delgado, M., & Martin-Bautista, M. J. (2019, August). A comparative analysis of tools for visualizing association rules: A proposal for visualising fuzzy association rules. In 2019 Conference of the International Fuzzy Systems Association and the European Society for Fuzzy Logic and Technology (EUSFLAT 2019). Atlantis Press. https://download.atlantis-press.com/article/125914842.pdf ↩
Zanin, M., Bergamaschi, C. L., Ferreira, J. R., Mendes, S. L., & Oliveira Moreira, D. (2019). Dog days are just starting: the ecology invasion of free-ranging dogs (Canis familiaris) in a protected area of the Atlantic Forest. European Journal of Wildlife Research, 65(5). https://doi.org/10.1007/s10344-019-1303-5 ↩
Luc, A., Lê, S., & Philippe, M. (2019). Nudging consumers for relevant data using Free JAR profiling: an application to product development. Food Quality and Preference, 103751. https://doi.org/10.1016/j.foodqual.2019.103751 ↩
Lennox, R. J., Veríssimo, D., Twardek, W. M., Davis, C. R., & Jarić, I. (2019). Sentiment analysis as a measure of conservation culture in scientific literature. Conservation Biology. https://doi.org/10.1111/cobi.13404 ↩
da Conceição António, N. M. (2019). Hotel Revenue Management: Using Data Science to Predict Booking Cancellations (Doctoral dissertation, ISCTE-IUL). http://bit.ly/2nWX50I ↩
Han, T., Zheng, Q., Onstein, R. E., Rojas‐Andrés, B. M., Hauenschild, F., Muellner‐Riehl, A. N., & Xing, Y. (2019). Polyploidy promotes species diversification of Allium through ecological shifts. New Phytologist. https://doi.org/10.1111/nph.16098 ↩
Dawson, A., Paciorek, C. J., Goring, S. J., Jackson, S. T., McLachlan, J. S., & Williams, J. W. (2019). Quantifying trends and uncertainty in prehistoric forest composition in the upper Midwestern United States. Ecology. https://doi.org/10.1002/ecy.2856 ↩
O’Farrell, S., Chollett, I., Sanchirico, J. N., & Perruso, L. (2019). Classifying fishing behavioral diversity using high-frequency movement data. Proceedings of the National Academy of Sciences, 201906766. https://doi.org/10.1073/pnas.1906766116 ↩
Hayden, B., Palomares, M. L. D., Smith, B. E., & Poelen, J. H. (2019). Biological and environmental drivers of trophic ecology in marine fishes - a global perspective. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-47618-2 ↩
Neugebauer, K., El‐Serehy, H. A., George, T. S., McNicol, J. W., Moraes, M. F., Sorreano, M. C. M., & White, P. J. (2019). The influence of phylogeny and ecology on root, shoot and plant ionomes of fourteen native Brazilian species. Physiologia Plantarum. https://doi.org/10.1111/ppl.13018 ↩
Wagner, J. (2019). Using Advanced Analytics to Predict Risk for Grants Oversight. Masters Thesis. https://jscholarship.library.jhu.edu/bitstream/handle/1774.2/61849/Wagner%2C%20Jennifer.pdf?sequence=1&isAllowed=y ↩
Pender, J. E., Hipp, A. L., Hahn, M., Kartesz, J., Nishino, M., & Starr, J. R. (2019). How sensitive are climatic niche inferences to distribution data sampling? A comparison of Biota of North America Program (BONAP) and Global Biodiversity Information Facility (GBIF) datasets. Ecological Informatics, 100991. https://doi.org/10.1016/j.ecoinf.2019.100991 ↩
Park, A. W. (2019). Food web structure selects for parasite host range. Proceedings of the Royal Society B: Biological Sciences, 286(1908), 20191277. https://doi.org/10.1098/rspb.2019.1277 ↩
Sánchez-Páez, D. A., & Ortega, J. A. (2019). Reported patterns of pregnancy termination from Demographic and Health Surveys. PLOS ONE, 14(8), e0221178. https://doi.org/10.1371/journal.pone.0221178 ↩
CRAN: GitHub:
v0.4.1) of cde is on CRAN - download data from the Catchment Data Explorer. Checkout the docs to get started. v0.1.0) of citecorp is on CRAN - client for the Open Citations Corpus. Checkout the docs to get started. v0.1.1) of PostcodesioR is on CRAN - API wrapper for Postcodes.io. Checkout the docs to get started. v0.6) of roadoi is on CRAN - find free versions of scholarly publications via Unpaywall. See the release notes for changes. Checkout the vignette to get started. new data fields in Unpaywall data; minor fixes
v7.6.1 & v7.6.2) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started. docs now at https://docs.ropensci.org/drake/; many bug fixes
v0.8.0 & v0.8.2) of pangaear is on CRAN - Client for the Pangaea database. See the release notes for changes. Checkout the vignette to get started. new object
pg_cacheto manage file caching;pg_data()now includes parsed metadata; bug fixes forpg_data()
v0.1.5) of gutenbergr is on CRAN - Download and process public domain works from Project Gutenberg. See the release notes for changes. Checkout the vignette to get started. replace
data_frame()w/tibble()
v0.2.8) of fingertipsR is on CRAN - Fingertips data for public health http://fingertips.phe.org.uk/. See the release notes for changes. Checkout the vignettes to get started. better failure behavior: throw informative message when no API response
v1.1.2) of nasapower is on CRAN - NASA POWER API Client. See the release notes for changes. Checkout the docs to get started. correct citation; suppress
APSIM::createMetFile()console output
v0.3.0) of oai is on CRAN - general purpose OAI-PMH services client. See the release notes for changes. Checkout the docs to get started.
id()gainsasparam;update_providers()fix; small changes
v1.2.6) of UCSCXenaTools is on CRAN - download and explore datasets from UCSC Xena data hubs. See the release notes for changes. Checkout the docs to get started. update pkg citation
v0.3.7) of jstor is on CRAN - read data from JSTOR/DfR. See the release notes for changes. Checkout the docs to get started.
tidyrcompatability; remove defunct fxns
v2.0.0) of GSODR is on CRAN - Global Surface Summary of the Day (GSOD) Weather Data from R. See the release notes for changes. Checkout the docs to get started.
get_GSOD()now using https rather than FTP; objects now returned as data.table objects; minor changes
v0.2.0) of jaod is on CRAN - Directory of Open Access Journals client. See the release notes for changes. Checkout the docs to get started. new vignette; docs changes
v0.3.1) of getCRUCLdata is on CRAN - use and explore CRU CL v. 2.0 climatology elements. See the release notes for changes. Checkout the docs to get started. fix documentation bug in an example
v0.2.3) of tradestatistics is on CRAN - open trade statistics api wrapper and utility program. See the release notes for changes. Checkout the docs to get started. fixes for testthat
v1.0.14) of lingtypology is on CRAN - linguistic typology and mapping. See the release notes for changes. Checkout the docs to get started. some dependencies moved to Suggests; new fxns
uralex.feature()andggmap.feature()
v2.2) of magick is on CRAN - Advanced graphics and Image-Processing in R. See the release notes for changes. Checkout the vignette to get started. new fxns
image_read_video(),image_separate(),image_combine(); improve RStudio auto preview
v2.0.3) of ijtiff is on CRAN - Comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started. add
libjpegneeds to SystemRequirements
v0.3) of av is on CRAN - working with audio and video. See the release notes for changes. Checkout the docs to get started. major refactor; new fxns
av_video_convert(),av_audio_convert(),av_video_images()
v0.7.2) of DataSpaceR is on CRAN - interface to the CAVD DataSpace. See the release notes for changes. Checkout the docs to get started. fix broken and invalid URLs
v0.3.0) of vcr is on CRAN - record HTTP calls to disk for test caching. See the release notes for changes. Checkout the HTTP testing book to get started. re-recording cassettes now works, see docs about setting a re-record interval; fixes to request body matching
v0.2.0) of handlr is on CRAN - Convert among citation formats. See the release notes for changes. Checkout the README to get started. new fxn
handl_to_df()(and associated method$as_df()onHandlClient) to convert ahandlobject to a data.frame
v0.5.0) of rnassqs is on CRAN - access the NASS Quick Stats API. See the release notes for changes. Checkout the docs to get started. change how queries are specified; simplified token management; docs improved
We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following three packages were recently submitted:
The following two packages recently went through our software-review process and have been approved:
Stefanie Butland wrote the second of a semi-monthly summary of the rOpenSci Newsletter including software reviews, packages on CRAN, use cases, posts from staff and community, and events - 2 Months in 2 Minutes - rOpenSci News, August 2019
Sam Tyner wrote a post describing her free online book on forensic science in R. This work was funded by a 2018 rOpenSci Research Fellowship. Read the post here: Introducing Open Forensic Science in R
Tiffany Timbers in a recent post Using rOpenSci Software Peer Review Guidelines for Teaching wrote about the Collaborative Software Development course she teaches at University of British Columbia. In this course, they recommend students use our book rOpenSci Packages: Development, Maintenance, and Peer Review; and the students and teachers use our Review Template when submitting and reviewing assignments.
Aldo Compagnoni wrote a post on his package that recently went through review, popler: Synthesizing population time-series data from the USA Long Term Ecological Research Network. Aldo talks about the motivation for making the package and the database behind the package.
The following 24 works use/cite rOpenSci software:
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had six recent examples of maintainer transitions within rOpenSci:
We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.
Saxena, P., Saxena, D., Nie, X., Helmers, A., Ramachandran, N., Sakib, N., & Ahamed, S. (2019). Feature Boosting in Natural Image Classification. 2019 IEEE 43rd Annual Computer Software and Applications Conference (COMPSAC). https://doi.org/10.1109/compsac.2019.10184 ↩
Pilogallo, A., Saganeiti, L., Scorza, F., & Murgante, B. (2019). Investigating Urban Growth Dynamic – Land Surface Temperature Relationship. Lecture Notes in Computer Science, 701–710. https://doi.org/10.1007/978-3-030-24302-9_51 ↩
Sang, Zihaohan. No-analog ecological communities since the last glacial maximum inferred from fossil pollen records for North America. Diss. University of Alberta, 2019. https://sites.ualberta.ca/~ahamann/people/pdfs/Sang_2019_MSc.pdf ↩
Xia, Liu, Zhang, & Guo. (2019). GEDS: A Gene Expression Display Server for mRNAs, miRNAs and Proteins. Cells, 8(7), 675. https://doi.org/10.3390/cells8070675 ↩
Burkett, Kaitlyn E. Who Is Ready To Retire: Your Average Life Expectancy And The Savings Needed To Support You. Diss. Appalachian State University, 2019. https://libres.uncg.edu/ir/asu/f/Burkett_Kaitlyn_2019_Thesis.pdf ↩
Valdez, J. W., & Mandrekar, K. (2019). Assessing the Species in the CARES Preservation Program and the Role of Aquarium Hobbyists in Freshwater Fish Conservation. https://doi.org/10.20944/preprints201907.0030.v1 ↩
Correia, R. A., Ruete, A., Stropp, J., Malhado, A. C. M., dos Santos, J. W., Lessa, T., … Ladle, R. J. (2019). Using ignorance scores to explore biodiversity recording effort for multiple taxa in the Caatinga. Ecological Indicators, 106, 105539. https://doi.org/10.1016/j.ecolind.2019.105539 ↩
Lin, C., Lou, Y.-S., Tsai, D.-J., Lee, C.-C., Hsu, C.-J., Wu, D.-C., … Fang, W.-H. (2019). Projection Word Embedding Model With Hybrid Sampling Training for Classifying ICD-10-CM Codes: Longitudinal Observational Study. JMIR Medical Informatics, 7(3), e14499. https://doi.org/10.2196/14499 ↩
Stöver, B. C., Wiechers, S., & Müller, K. F. (2019). JPhyloIO: a Java library for event-based reading and writing of different phylogenetic file formats through a common interface. BMC Bioinformatics, 20(1). https://doi.org/10.1186/s12859-019-2982-3 ↩
Myers, E. A., Xue, A. T., Gehara, M., Cox, C., Davis Rabosky, A. R., Lemos‐Espinal, J., … Burbrink, F. T. (2019). Environmental Heterogeneity and Not Vicariant Biogeographic Barriers Generate Community Wide Population Structure in Desert Adapted Snakes. Molecular Ecology. https://doi.org/10.1111/mec.15182 ↩
Van Schaik, P., Peng, Y., Ojelabi, A., & Ling, J. (2019). Explainable statistical learning in public health for policy development: the case of real-world suicide data. BMC medical research methodology, 19(1), 152. https://bmcmedresmethodol.biomedcentral.com/articles/10.1186/s12874-019-0796-7 ↩
Hagen, O., Vaterlaus, L., Albouy, C., Brown, A., Leugger, F., Onstein, R. E., … Pellissier, L. (2019). Mountain building, climate cooling and the richness of cold‐adapted plants in the Northern Hemisphere. Journal of Biogeography. https://doi.org/10.1111/jbi.13653 ↩
Carlström, K. E., Ewing, E., Granqvist, M., Gyllenberg, A., Aeinehband, S., Enoksson, S. L., … Piehl, F. (2019). Therapeutic efficacy of dimethyl fumarate in relapsing-remitting multiple sclerosis associates with ROS pathway in monocytes. Nature Communications, 10(1). https://doi.org/10.1038/s41467-019-11139-3 ↩
Dag, O., Karabulut, E., & Alpar, R. (2019). GMDH2: Binary Classification via GMDH-Type Neural Network Algorithms—R Package and Web-Based Tool. International Journal of Computational Intelligence Systems, 12(2), 649. https://doi.org/10.2991/ijcis.d.190618.001 ↩
Wüest, R. O., Zimmermann, N. E., Zurell, D., Alexander, J. M., Fritz, S. A., Hof, C., … Karger, D. N. (2019). Macroecology in the age of Big Data – Where to go from here? Journal of Biogeography. https://doi.org/10.1111/jbi.13633 ↩
Saunders, K. R., Stephenson, A. G., & Karoly, D. J. (2019). A Regionalisation Approach for Rainfall based on Extremal Dependence. arXiv preprint https://arxiv.org/pdf/1907.05750.pdf ↩
Collins, R. A., Bakker, J., Wangensteen, O. S., Soto, A. Z., Corrigan, L., Sims, D. W., … Mariani, S. (2019). Non‐specific amplification compromises environmental DNA metabarcoding with COI. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13276 ↩
Elsner, J. B., & Schroder, Z. (2019, July 18). Tornado damage ratings estimated with cumulative logistic regression. https://doi.org/10.31223/osf.io/k9wv6 ↩
Abhilash, L., & Sheeba, V. (2019). RhythmicAlly: Your R and Shiny–Based Open-Source Ally for the Analysis of Biological Rhythms. Journal of Biological Rhythms, 074873041986247. https://doi.org/10.1177/0748730419862474 ↩
Peters, A., Delhey, K., Nakagawa, S., Aulsebrook, A., & Verhulst, S. (2019). Immunosenescence in wild animals: meta‐analysis and outlook. Ecology Letters. https://doi.org/10.1111/ele.13343 ↩
Die, J. V., Elmassry, M. M., LeBlanc, K. H., Awe, O. I., Dillman, A., & Busby, B. (2019). geneHummus: an R package to define gene families and their expression in legumes and beyond. BMC Genomics, 20(1). https://doi.org/10.1186/s12864-019-5952-2 ↩
Saadi, M., Oudin, L., & Ribstein, P. (2019). Random Forest Ability in Regionalizing Hourly Hydrological Model Parameters. Water, 11(8), 1540. https://doi.org/10.3390/w11081540 ↩
Jaganathan, G. K., & Dalrymple, S. E. (2019). Internal Seed Structure of Alpine Plants and Extreme Cold Exposure. Data, 4(3), 107. https://doi.org/10.3390/data4030107 ↩
Alhajeri, B. H., Porto, L., & Maestri, R. (2019). Habitat productivity is a poor predictor of body size in rodents. Current Zoology. https://academic.oup.com/cz/advance-article/doi/10.1093/cz/zoz037/5539488 ↩
CRAN: GitHub:
There’s very little activity in this section because CRAN submissions were closed for the last week and a half.
v0.4.0) of webmockr is on CRAN - stubbing and setting expectations on HTTP requests. See the release notes for changes. Checkout the HTTP testing book to get started. fix link to package manual; fix single method request matching
v0.5.19) of aRxiv is on CRAN - Interface to the arXiv API. See the release notes for changes. Checkout the docs to get started. update vignette; add ORCIDs to DESCRIPTION
We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following package was recently submitted:
The following package recently went through our software-review process and has been approved:
The following 19 works use/cite rOpenSci software:
In a recent blog post Being a better programmer and scientist with rOpenSci Matt Boone of the Mablab at University of Florida (and an author on the refnet package under rOpenSci review) wrote about R and programming, and did a nice job of describing our software review system.
In an August 15th article in Forbes Restrict Twice-As-Deadly SUVs In U.K. Cities, Urge Transport Data Scientists, the data used was from the stplanr package maintained by Robin Lovelace and others. See also Robin’s tweet about the article.
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
![\"fingertips_use_case\"](\"https://news.ropensci.org/assets/img/fingertips_use_case.png\")
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had six recent examples of maintainer transitions within rOpenSci:
We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.
Yen, Y., Zhao, P., & Sohail, M. T. (2019). The morphology and circuity of walkable, bikeable, and drivable street networks in Phnom Penh, Cambodia. Environment and Planning B: Urban Analytics and City Science, 239980831985772. https://doi.org/10.1177/2399808319857726 ↩
Danella Figo, D., De Amicis, K., Neiva Santos de Aquino, D., Pomiecinski, F., Gadermaier, G., Briza, P., … Souza Santos, K. (2019). Cashew Tree Pollen: An Unknown Source of IgE-Reactive Molecules. International Journal of Molecular Sciences, 20(10), 2397. https://doi.org/10.3390/ijms20102397 ↩
Kanterakis, G., Skoulikaris, C., & Dimitriou, E. Assessment of hydrological modelling behaviour at basin scale on the number of delineated sub-basins. Proceedings of the Seventh International Conference on Environmental Management, Engineering, Planning & Economics https://www.researchgate.net/profile/Charalampos_Skoulikaris/publication/333652500_Assessment_of_hydrological_modelling_behaviour_at_basin_scale_on_the_number_of_delineated_sub-basins/links/5cfa46ba4585157d15991da1/Assessment-of-hydrological-modelling-behaviour-at-basin-scale-on-the-number-of-delineated-sub-basins.pdf ↩
Petrik, C. M., Stock, C. A., Andersen, K. H., van Denderen, P. D., & Watson, J. R. (2019). Bottom-up drivers of global patterns of demersal, forage, and pelagic fishes. Progress in Oceanography, 176, 102124. https://doi.org/10.1016/j.pocean.2019.102124 ↩
Calderone, A. (2019). A Computational Analysis of Natural Languages to Build a Sentence Structure Aware Artificial Neural Network. arXiv preprint arXiv:1906.05491 https://arxiv.org/pdf/1906.05491.pdf ↩
Uzma, Jiménez-Mejías, P., Amir, R., Hayat, M. Q., & Hipp, A. L. (2019). Timing and ecological priority shaped the diversification of sedges in the Himalayas. PeerJ, 7, e6792. https://doi.org/10.7717/peerj.6792 ↩
Baylis, A. M. M., Tierney, M., Orben, R. A., Warwick-Evans, V., Wakefield, E., Grecian, W. J., … Brickle, P. (2019). Important At-Sea Areas of Colonial Breeding Marine Predators on the Southern Patagonian Shelf. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-44695-1 ↩
Nourbakhsh, M., Mansoor, A., Koro, K., Zhang, Q., & Minoo, P. (2019). Expression Profiling Reveals Involvement of WNT Pathway in the Malignant Progression of Sessile Serrated Adenomas. The American Journal of Pathology. https://doi.org/10.1016/j.ajpath.2019.05.009 ↩
Waller, J. (2019). Data Location Quality at GBIF. Biodiversity Information Science and Standards, 3. https://doi.org/10.3897/biss.3.35829 ↩
Shackleton, M. E., Rees, G. N., Watson, G., Campbell, C., & Nielsen, D. (2019). Environmental DNA reveals landscape mosaic of wetland plant communities. Global Ecology and Conservation, 19, e00689. https://doi.org/10.1016/j.gecco.2019.e00689 ↩
Nelli, L., Ferguson, H. M., & Matthiopoulos, J. (2019). Achieving explanatory depth and spatial breadth in infectious disease modelling: Integrating active and passive case surveillance. Statistical Methods in Medical Research, 096228021985638. https://doi.org/10.1177/0962280219856380 ↩
Glicksberg, B. S., Oskotsky, B., Thangaraj, P. M., Giangreco, N., Badgeley, M. A., Johnson, K. W., … Butte, A. J. (2019). PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model. Bioinformatics. https://doi.org/10.1093/bioinformatics/btz409 ↩
Brown, E. E., Rashidi‐Ranjbar, N., Caravaggio, F., Gerretsen, P., Pollock, B. G., … Mulsant, B. H. (2019). Brain Amyloid PET Tracer Delivery is Related to White Matter Integrity in Patients with Mild Cognitive Impairment. Journal of Neuroimaging. https://doi.org/10.1111/jon.12646 ↩
Koppelstaetter, C., Leierer, J., Rudnicki, M., Kerschbaum, J., Kronbichler, A., Melk, A., … Perco, P. (2019). Computational Drug Screening Identifies Compounds Targeting Renal Age-associated Molecular Profiles. Computational and Structural Biotechnology Journal, 17, 843–853. https://doi.org/10.1016/j.csbj.2019.06.019 ↩
Calero Valdez A., Ziefle M. (2019) Trends and Changes in the Field of HCI the Last Decade from the Perspective of HCII Conference. In: Kurosu M. (eds) Human-Computer Interaction. Perspectives on Design. HCII 2019. Lecture Notes in Computer Science, vol 11566. Springer, Cham https://doi.org/10.1007/978-3-030-22646-6_3 ↩
Alfaro, M. E., Karan, E., Schwartz, S. T., & Shultz, A. J. (2019). The Evolution of Color Pattern in Butterflyfishes (Chaetodontidae). Integrative and comparative biology. https://academic.oup.com/icb/advance-article-abstract/doi/10.1093/icb/icz119/5530961 ↩
Butterfield, B. J., Holmgren, C. A., Anderson, R. S., & Betancourt, J. L. (2019). Life history traits predict colonization and extinction lags of desert plant species since the Last Glacial Maximum. Ecology. https://doi.org/10.1002/ecy.2817 ↩
Kovalenko, K. E., Johnson, L. B., Brady, V. J., Ciborowski, J. J. H., Cooper, M. J., Gathman, J. P., … Uzarski, D. G. (2019). Hotspots and bright spots in functional and taxonomic fish diversity. Freshwater Science, 000–000. https://doi.org/10.1086/704713 ↩
Ferraz, M. de A. M. M., Carothers, A., Dahal, R., Noonan, M. J., & Songsasen, N. (2019). Oviductal extracellular vesicles interact with the spermatozoon’s head and mid-piece and improves its motility and fertilizing ability in the domestic cat. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-45857-x ↩
CRAN: GitHub:
v1.7) of tidypmc is on CRAN - parse full text XML documents from PubMed Central. Checkout the vignettes to get started. v1.2.5) of UCSCXenaTools is on CRAN - download and explore datasets from UCSC Xena data hubs. Checkout the docs to get started. v0.8.4) of crul is on CRAN - an R6 based HTTP client for R made for developers. See the release notes for changes. Checkout the docs to get started. (Windows users please do upgrade: no longer set cainfo curl option); improve parse method in HttpResponse class
v1.22) of rtika is on CRAN - R Interface to Apache Tika. See the release notes for changes. Checkout the docs to get started. update Tika to 1.22
v0.3.0) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. new fxns:
od_to_odmatrix(),odmatrix_to_od(),od_oneway(), and many newod_id*()fxns; new vignette
v0.1.3) of gitignore is on CRAN - create useful .gitignore files for your project. See the release notes for changes. Checkout the docs to get started. fix cran check problems
v1.0.0) of stats19 is on CRAN - Work with Open Road Traffic Casualty Data from Great Britain. See the release notes for changes. Checkout the docs to get started. now much easier to download STATS19 data w/
dl_stats19()
v0.5.0) of brranching is on CRAN - Fetch Phylogenies from Many Sources. See the release notes for changes. Checkout the vignette to get started. now using pkg conditionz to make messages less frequent when user does not have an API key for NCBI
v0.1.2) of geoparser is on CRAN - interface to the Geoparser.io API. See the release notes for changes. Checkout the docs to get started. fix error caused by namespace issue;
geoparser_key()fails better when no key avail.
v0.0.3) of plotdap is on CRAN - easily visualize data from ERDDAP servers via the rerddap package. See the release notes for changes. Checkout the vignette to get started. v2.1) of magick is on CRAN - Advanced graphics and Image-Processing in R. See the release notes for changes. Checkout the vignette to get started. new docs site; many fixes
v4.1) of tesseract is on CRAN - bindings to Tesseract, an OCR engine https://opensource.google.com/projects/tesseract. See the release notes for changes. Checkout the vignette to get started. fix memory leak in
ocr_data; update to libtesseract 4.1.0
v0.1.4) of phylocomr is on CRAN - Interface to Phylocom for analysis of phylogenetic community structure and character evolution. See the release notes for changes. Checkout the vignette to get started. fix some non-working examples; fixes to internal type checking; fix C lib error
v0.3.0) of ckanr is on CRAN - R client for the CKAN API. See the release notes for changes. Checkout the docs to get started. big release, first in 4 years: new pkg maintainer; many new fxns; many fxns w/ changed params; fxn name changes
We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following five packages were recently submitted:
The following package recently went through our software-review process and has been approved:
The following 15 works use/cite rOpenSci software:
Dan Quintana gives a short video demonstration of using europepmc, a package maintained by Najko Jahn
Ever wanted to visualize the popularity of a research topic over time? Here's how, using the 'europepmc' #Rstats package
— Dan Quintana (@dsquintana) July 23, 2019
YouTube link: https://t.co/fI5B6PLDco
Code: https://t.co/hSnYiBrUh8
Thread 👇 pic.twitter.com/Ezsh9jUJul
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had six recent examples of maintainer transitions within rOpenSci:
We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.
Wright, R. J., Gibson, M. I., & Christie-Oleza, J. A. (2019). Understanding microbial community dynamics to improve optimal microbiome selection. Microbiome, 7(1). https://doi.org/10.1186/s40168-019-0702-x ↩
Meisner, J., Clifford, W. R., Wohrle, R. D., Kangiser, D., & Rabinowitz, P. (2019). Soil and climactic predictors of canine coccidioidomycosis seroprevalence in Washington State: an ecological cross‐sectional study. Transboundary and Emerging Diseases. https://doi.org/10.1111/tbed.13265 ↩
Tetzlaff, S. J., Sperry, J. H., & DeGregorio, B. A. (2019). Effects of antipredator training, environmental enrichment, and soft release on wildlife translocations: A review and meta-analysis. Biological Conservation, 236, 324–331. https://doi.org/10.1016/j.biocon.2019.05.054 ↩
Alhajeri, B. H., & Fourcade, Y. (2019). High correlation between species‐level environmental data estimates extracted from IUCN expert range maps and from GBIF occurrence data. Journal of Biogeography. https://doi.org/10.1111/jbi.13619 ↩
Boggs, Scheible, Machado, & Meiklejohn. (2019). Single Fragment or Bulk Soil DNA Metabarcoding: Which is Better for Characterizing Biological Taxa Found in Surface Soils for Sample Separation? Genes, 10(6), 431. https://doi.org/10.3390/genes10060431 ↩
Ros-Candeira, A., Pérez-Luque, A. J., Suárez-Muñoz, M., Bonet-García, F. J., Hódar, J. A., Giménez de Azcárate, F., & Ortega-Díaz, E. (2019). Dataset of occurrence and incidence of pine processionary moth in Andalusia, south Spain. ZooKeys, 852, 125–136. https://doi.org/10.3897/zookeys.852.28567 ↩
Van Denderen, D., Gislason, H., & Andersen, K. H. (2019). Little difference in average fish growth and maximum size across temperatures. EcoEvoRxiv. https://doi.org/10.32942/osf.io/8cu4y ↩
Bailey, L. D., Ens, B. J., Both, C., Heg, D., Oosterbeek, K., & van de Pol, M. (2019). Habitat selection can reduce effects of extreme climatic events in a long‐lived shorebird. Journal of Animal Ecology. https://doi.org/10.1111/1365-2656.13041 ↩
Palacios-Abrantes, J., Cisneros-Montemayor, A. M., Cisneros-Mata, M. A., Rodríguez, L., Arreguín-Sánchez, F., Aguilar, V., … Cheung, W. W. L. (2019). A metadata approach to evaluate the state of ocean knowledge: Strengths, limitations, and application to Mexico. PLOS ONE, 14(6), e0216723. https://doi.org/10.1371/journal.pone.0216723 ↩
McTavish, E. J. (2019). Linking Biodiversity Data Using Evolutionary History. Biodiversity Information Science and Standards, 3. https://doi.org/10.3897/biss.3.36207 ↩
Nyboer, E. A., Liang, C., & Chapman, L. J. (2019). Assessing the vulnerability of Africa’s freshwater fishes to climate change: A continent-wide trait-based analysis. Biological Conservation, 236, 505–520. https://doi.org/10.1016/j.biocon.2019.05.003 ↩
Krah, F.-S., & Heibl, C. (2019). rGUIDANCE – alignment confidence score computation in R. Journal of Open Source Software, 4(36), 1350. https://doi.org/10.21105/joss.01350 ↩
Morelle, K., Jezek, M., Licoppe, A., & Podgorski, T. (2019). Deathbed choice by ASF‐infected wild boar can help find carcasses. Transboundary and Emerging Diseases. https://doi.org/10.1111/tbed.13267 ↩
Grattarola, F., Botto, G., da Rosa, I., Gobel, N., González, E., González, J., … Pincheira-Donoso, D. (2019). Biodiversidata: An Open-Access Biodiversity Database for Uruguay. Biodiversity Data Journal, 7. https://doi.org/10.3897/bdj.7.e36226 ↩
Kravchuk, O. I., Lyupina, Y. V., Erokhov, P. A., Finoshin, A. D., Adameyko, K. I., Mishyna, M. Y., … Mikhailov, V. S. (2019). Characterization of the 20S proteasome of the lepidopteran, Spodoptera frugiperda. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. https://doi.org/10.1016/j.bbapap.2019.06.010 ↩
CRAN: GitHub:
v7.5.2) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started. remove accidental creation of a dot file
v0.6.4/v0.6.5) of rerddap is on CRAN - General Purpose Client for ERDDAP Servers. See the release notes for changes. Checkout the vignettes to get started. fix internal http request error handler; fix a test
v1.0.4) of available is on CRAN - check if the title of a package is available. See the release notes for changes. Checkout the README to get started. tests requiring network access are not skipped on CRAN
v1.2) of cld3 is on CRAN - Bindings to Google’s Compact Language Detector 3. See the release notes for changes. Checkout the docs to get started. update to protobuf 3.8 for windows; suppress warnings about pragmas in autogen protobuf headers
v0.2.7) of fingertipsR is on CRAN - Fingertips data for public health http://fingertips.phe.org.uk/. See the release notes for changes. Checkout the vignettes to get started. add option
AreaTypeId=\"Allinfingertips_data(); added param toarea_types(); change tocategory_types(); add http request retry
v0.2.0) of vitae is on CRAN - R Markdown Resumes and CVs. See the release notes for changes. Checkout the docs to get started. theme support for moderncv; other template changes; breaking change to
bibliography_entries
v2.0.2) of ijtiff is on CRAN - Comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started. bug fixes
v0.6.0) of bomrang is on CRAN - Australian government Bureau of Meteorology (BOM) data. See the release notes for changes. Checkout the docs to get started. many bug fixes
v0.26.1) of git2r is on CRAN - an interface to the libgit2 library, a pure C implementation of the Git core methods. See the release notes for changes. Checkout the README to get started. fixed the broken build on Solaris on CRAN
v0.4.2) of traits is on CRAN - species trait data from around the web. See the release notes for changes. Checkout the README to get started. minor betydb change;
taxa_search()breaking change (Traitbank service completely changed)
v0.8.0) of crul is on CRAN - an R6 based HTTP client for R made for developers. See the release notes for changes. Checkout the docs to get started. can now pass params through
parse()toiconv(); use httpcode pkg instead of fauxpas insideok()
v0.2.0) of grainchanger is on CRAN - Data aggregation methods for raster data. See the release notes for changes. Checkout the docs to get started. v0.9.8) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started. new fxn
taxize_options; allget_*fxns gain ability to track progress and restart in case of interruption - & prettier progress and summary info; bug fixes
v0.4.0) of worrms is on CRAN - client for World Register of Marine Species. See the release notes for changes. Checkout the vignette to get started. new fxns
wm_ranks_id()/wm_ranks_name()for getting taxonomic ranks by rank identifier or rank name; new fxnwm_records_rank()for getting AphiaRecords for a given rank id
v0.9.0) of bold is on CRAN - interface to Bold Systems (http://www.boldsystems.org/) API. See the release notes for changes. Checkout the vignette to get started. allow curl options to be passed into
bold_identify_parents(); bug fix inbold_identify()
v1.3.0) of fulltext is on CRAN - full text of scholarly articles across many data sources. See the release notes for changes. Checkout the fulltext book to get started.
ft_get()gains new data source: ScienceDirect;ft_get()performance improvements; curl options can now be passed through nearly all fxns
v3.0.4) of rfishbase is on CRAN - interface to Fishbase data. See the release notes for changes. Checkout the docs to get started. use latest data version
v1.1.0) of jsonvalidate is on CRAN - Validate JSON. See the release notes for changes. Checkout the docs to get started. We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following two packages recently went through our software-review process and have been approved:
Stefanie Butland wrote about folks talking about rOpenSci projects at useR in Toulouse, France. The conference already happened; slides are linked from the talk schedule page, and video of talks may be up later.
Laura Graham wrote about her R package that recently went through software review Aggregating spatial data with the grainchanger package. grainchanger facilitates spatial data aggregation.
![](\"../assets/img/grainchainger-logo.png\"){kind=logo}
The following 20 works use/cite rOpenSci software:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had six recent examples of maintainer transitions within rOpenSci:
We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.
Steidinger, B. S., Crowther, T. W., Liang, J., Van Nuland, M. E., Werner, G. D. A., … Peay, K. G. (2019). Climatic controls of decomposition drive the global biogeography of forest-tree symbioses. Nature, 569(7756), 404–408. https://doi.org/10.1038/s41586-019-1128-0 ↩
Mitchell, J. M. (2019). Computational Tools for the Untargeted Assignment of FT-MS Metabolomics Datasets. Dissertation. https://uknowledge.uky.edu/cgi/viewcontent.cgi?article=1042&context=biochem_etds ↩
Bagley, M., Pilgrim, E., Knapp, M., Yoder, C., Santo Domingo, J., & Banerji, A. (2019). High-throughput environmental DNA analysis informs a biological assessment of an urban stream. Ecological Indicators, 104, 378–389. https://doi.org/10.1016/j.ecolind.2019.04.088 ↩
Foisy, M. R., Albert, L. P., Hughes, D. W. W., & Weber, M. G. (2019). Do latex and resin canals spur plant diversification? Re‐examining a classic example of escape and radiate coevolution. Journal of Ecology. https://doi.org/10.1111/1365-2745.13203 ↩
Ogłuszka, M., Orzechowska, M., Jędroszka, D., Witas, P., & Bednarek, A. K. (2019). Evaluate Cutpoints: Adaptable continuous data distribution system for determining survival in Kaplan-Meier estimator. Computer Methods and Programs in Biomedicine, 177, 133–139. https://doi.org/10.1016/j.cmpb.2019.05.023 ↩
Westmeijer, G., Everaert, G., Pirlet, H., De Clerck, O., & Vandegehuchte, M. B. (2019). Mechanistic niche modelling to identify favorable growth sites of temperate macroalgae. Algal Research, 41, 101529. https://doi.org/10.1016/j.algal.2019.101529 ↩
Kortz, A. R., & Magurran, A. E. (2019). Increases in local richness (α-diversity) following invasion are offset by biotic homogenization in a biodiversity hotspot. Biology Letters, 15(5), 20190133. https://doi.org/10.1098/rsbl.2019.0133 ↩
Pérez-Palma, E., Gramm, M., Nürnberg, P., May, P., & Lal, D. (2019). Simple ClinVar: an interactive web server to explore and retrieve gene and disease variants aggregated in ClinVar database. Nucleic Acids Research. https://doi.org/10.1093/nar/gkz411 ↩
Green, E. P., Whitcomb, A., Kahumbura, C., Rosen, J. G., Goyal, S., Achieng, D., & Bellows, B. (2019). What is the best method of family planning for me?: a text mining analysis of messages between users and agents of a digital health service in Kenya. Gates Open Research, 3, 1475. https://doi.org/10.12688/gatesopenres.12999.1 ↩
Mihalitsis, M., & Bellwood, D. R. (2019). Morphological and functional diversity of piscivorous fishes on coral reefs. Coral Reefs. https://doi.org/10.1007/s00338-019-01820-w ↩
Kannenberg, S. A., Novick, K. A., Alexander, M. R., Maxwell, J. T., Moore, D. J. P., Phillips, R. P., & Anderegg, W. R. L. (2019). Linking drought legacy effects across scales: From leaves to tree rings to ecosystems. Global Change Biology. https://doi.org/10.1111/gcb.14710 ↩
Aspillaga, E., Safi, K., Hereu, B., & Bartumeus, F. (2019). Modelling the three‐dimensional space use of aquatic animals combining topography and Eulerian telemetry data. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13232 ↩
Gibson, K. M., Nguyen, B. N., Neumann, L. M., Miller, M., Buss, P., Daniels, S., … Pukazhenthi, B. (2019). Gut microbiome differences between wild and captive black rhinoceros – implications for rhino health. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-43875-3 ↩
Sinval, J., Sirgy, M. J., Lee, D.-J., & Marôco, J. (2019). The Quality of Work Life Scale: Validity Evidence from Brazil and Portugal. Applied Research in Quality of Life. https://doi.org/10.1007/s11482-019-09730-3 ↩
Iserman, M., Nalabandian, T., & Ireland, M. (2019, June). Dictionaries and Decision Trees for the 2019 CLPsych Shared Task. In Proceedings of the Sixth Workshop on Computational Linguistics and Clinical Psychology (pp. 188-194). https://www.aclweb.org/anthology/W19-3025 ↩
Goodman, M. C., Hannah, S. M., & Ruttenberg, B. I. (2019). The relationship between geographic range extent, sea surface temperature and adult traits in coastal temperate fishes. Journal of Biogeography. https://doi.org/10.1111/jbi.13595 ↩
Fioravanti, G., Piervitali, E., & Desiato, F. (2019). A new homogenized daily data set for temperature variability assessment in Italy. International Journal of Climatology. https://doi.org/10.1002/joc.6177 ↩
Logemann, A., Schafberg, M., & Brockmeyer, B. (2019). Using the HPTLC-bioluminescence bacteria assay for the determination of acute toxicities in marine sediments and its eligibility as a monitoring assessment tool. Chemosphere. https://doi.org/10.1016/j.chemosphere.2019.05.246 ↩
Al-Mustanjid, A. (2019). Design of a common pathway drug for all types of cardiovascular diseases: A network biology approach. Network Biology, 9(2), 28. http://www.iaees.org/publications/journals/nb/articles/2019-9(2)/design-of-a-common-pathway-drug-for-cardiovascular-diseases.pdf ↩
Wambui, K. M., & Musenge, E. (2019). A space-time analysis of recurrent malnutrition-related hospitalisations in Kilifi, Kenya for children under-5 years. BMC Nutrition, 5(1). https://doi.org/10.1186/s40795-019-0296-5 ↩
CRAN: GitHub:
v0.1) of git2rdata is on CRAN - store and retrieve data.frames in a Git repository. Checkout the docs to get started. v0.3.3) of auk is on CRAN - eBird data extraction and processing. See the release notes for changes. Checkout the docs to get started. fixes to
auk_date(),auk_protocol(), andauk_set_awk_path()
v1.3.9) of MODIStsp is on CRAN - Automate Download and Preprocessing of MODIS Land Products Data. See the release notes for changes. Checkout the docs to get started. fixes bug causing crashes on MOD14A1 product; adds support for product MCD12Q2
v1.21) of rtika is on CRAN - R Interface to Apache Tika. See the release notes for changes. Checkout the docs to get started. v1.0.7) of skimr is on CRAN - compact and flexible summaries of data. See the release notes for changes. Checkout the vignettes to get started. stop assignment of foreign functions in namesspace at build time
v3.0.9) of rotl is on CRAN - an interface to the Open Tree of Life API. See the release notes for changes. Checkout the vignettes to get started. small fixes following updates to the Open Tree of Life API
v2.0.0) of ijtiff is on CRAN - Comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started.
get_tiff_tags_reference()->tif_tags_reference()&count_imgs()->count_frames(); now can read certain frames of a TIFF image w/read_tif()
We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following package was recently submitted:
The following two packages recently went through our software-review process and have been approved:
Scott Chamberlain, Maëlle Salmon, and Noam Ross wrote about Taking over maintenance of a software package. This blog post is about trying to give guidance to software contributors, and to rOpenSci editors, on how to deal with software maintainer changes.
Stefanie Butland wrote about our next community call: Community Call - Involving Multilingual Communities - coming up on June 28th.
Stefanie Butland wrote the first of a semi-monthly summary of the rOpenSci Newsletter including software reviews, packages on CRAN, use cases, posts from staff and community, and events - 2 Months in 2 Minutes - rOpenSci News, June 2019
The following 16 works use/cite rOpenSci software:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had six recent examples of maintainer transitions within rOpenSci:
We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
Ben Marwick started a discussion thread recently titled Teaching with the TIER protocol and replication assignments using R. All are welcome to contribute to the discussion.
Płaczek, A., Płuciennik, A., Pach, M., Jarząb, M., & Mrozek, D. (2019). The Role of Feature Selection in Text Mining in the Process of Discovering Missing Clinical Annotations – Case Study. Communications in Computer and Information Science, 248–262. https://doi.org/10.1007/978-3-030-19093-4_19 ↩
Germon, A., Jourdan, C., Bordron, B., Robin, A., Nouvellon, Y., Chapuis-Lardy, L., … Laclau, J.-P. (2019). Consequences of clear-cutting and drought on fine root dynamics down to 17 m in coppice-managed eucalypt plantations. Forest Ecology and Management, 445, 48–59. https://doi.org/10.1016/j.foreco.2019.05.010 ↩
Chambault, P., Baudena, A., Bjorndal, K. A., AR Santos, M., Bolten, A. B., & Vandeperre, F. (2019). Swirling in the ocean: immature loggerhead turtles seasonally target old anticyclonic eddies at the fringe of the North Atlantic gyre. Progress in Oceanography. https://doi.org/10.1016/j.pocean.2019.05.005 ↩
Kadereit, J. W., Lauterbach, M., Kandziora, M., Spillmann, J., & Nyffeler, R. (2019). Dual colonization of European high-altitude areas from Asia by Callianthemum (Ranunculaceae). Plant Systematics and Evolution. https://doi.org/10.1007/s00606-019-01583-5 ↩
Ktenioudaki, A., O’Donnell, C. P., & do Nascimento Nunes, M. C. (2019). Modelling the biochemical and sensory changes of strawberries during storage under diverse relative humidity conditions. Postharvest Biology and Technology, 154, 148–158. https://doi.org/10.1016/j.postharvbio.2019.04.023 ↩
Adeola, A. M., Botai, J. O., Mukarugwiza Olwoch, J., DeW. Rautenbach, H. C. J., Adisa, O. M., De Jager, C., … Aaron, M. (2019). Predicting malaria cases using remotely sensed environmental variables in Nkomazi, South Africa. Geospatial Health, 14(1). https://doi.org/10.4081/gh.2019.676 ↩
Salazar, P. C., Navarro-Cerrillo, R. M., Cruz, G., Grados, N., & Villar, R. (2019). Variability in growth and biomass allocation and the phenotypic plasticity of seven Prosopis pallida populations in response to water availability. Trees. https://doi.org/10.1007/s00468-019-01868-9 ↩
Best, B. D., & Halpin, P. N. (2019). Minimizing wildlife impacts for offshore wind energy development: Winning tradeoffs for seabirds in space and cetaceans in time. PLOS ONE, 14(5), e0215722. https://doi.org/10.1371/journal.pone.0215722 ↩
Mann, C. M., Martínez-Gálvez, G., Welker, J. M., Wierson, W. A., Ata, H., Almeida, M. P., … Dobbs, D. (2019). The Gene Sculpt Suite: a set of tools for genome editing. Nucleic Acids Research. https://doi.org/10.1093/nar/gkz405 ↩
da Silva, L. T., de Oliveira, I. L., Dantas, T., & Miranda, V. G. 2019. Studies of new data sources and techniques to improve CPI compilation in Brazil. 16th meeting of the Ottawa Group, Rio de Janeiro, Brazil. https://eventos.fgv.br/sites/eventos.fgv.br/files/arquivos/u161/study_of_new_data_sources_snipc_lincoln_da_silva.pdf ↩
Lin, B. Y., Chan, P. P., & Lowe, T. M. (2019). tRNAviz: explore and visualize tRNA sequence features. Nucleic Acids Research. https://doi.org/10.1093/nar/gkz438 ↩
Salecker, Jan; Dislich, Claudia; Wiegand, Kerstin; Meyer, Katrin M.; Pe’er,Guy (2019) : EFForTS-LGraf: A landscape generator for creating smallholder-driven land-use mosaics, EFForTS Discussion Paper Series, No. 29, Collaborative Research Centre990 - EFForTS, Ecological and Socioeconomic Functions of Tropical Lowland RainforestTransformation Systems. https://www.econstor.eu/bitstream/10419/196610/1/1665217219.pdf ↩
Comrie, B. (2019). Mapping the World’s Languages: From Data via Purpose to Representation. Handbook of the Changing World Language Map, 1–16. https://doi.org/10.1007/978-3-319-73400-2_131-1 ↩
Sporbert, M., Bruelheide, H., Seidler, G., Keil, P., Jandt, U., Austrheim, G., … Welk, E. (2019). Assessing sampling coverage of species distribution in biodiversity databases. Journal of Vegetation Science. https://doi.org/10.1111/jvs.12763 ↩
Vantas, K., Sidiropoulos, E., & Loukas, A. (2019). Robustness Spatiotemporal Clustering and Trend Detection of Rainfall Erosivity Density in Greece. Water, 11(5), 1050. https://doi.org/10.3390/w11051050 ↩
Schubert, M., Marcussen, T., Meseguer, A. S., & Fjellheim, S. (2019). The grass subfamily Pooideae: Cretaceous–Palaeocene origin and climate‐driven Cenozoic diversification. Global Ecology and Biogeography. https://doi.org/10.1111/geb.12923 ↩
CRAN: GitHub:
v1.0) of jenkins is on CRAN - Simple Jenkins Client for R. Checkout the README to get started. v2.0.14) of beastier is on CRAN - Provides a way to call BEAST2 from R. Checkout the docs to get started. v0.1.0) of colocr is on CRAN - conduct co-localization analysis of fluorescence microscopy images. Checkout the vignette to get started. v0.0.2) of plotdap is on CRAN - easily visualize data from ERDDAP servers via the rerddap package. Checkout the vignette to get started. v0.2.0) of ramlegacy is on CRAN - download and read RAM legacy stock assessment database. Checkout the docs to get started. v0.1.0) of rromeo is on CRAN - access publisher copyright & self-archiving policies via the SHERPA/RoMEO API. Checkout the docs to get started. v0.1.1) of tidync is on CRAN - a tidy approach to NetCDF data exploration and extraction. Checkout the docs to get started. v2.0.0) of ijtiff is on CRAN - Comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started. a few fxns changed names
v7.4.0) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started. data splitting; URL tracking; advanced memory management
v0.2.6) of fingertipsR is on CRAN - Fingertips data for public health http://fingertips.phe.org.uk/. See the release notes for changes. Checkout the vignettes to get started. bug fixes for
nearest_neighbours()andindicator_order()
v0.5.0) of rorcid is on CRAN - Interface to the Orcid.org API. See the release notes for changes. Checkout the vignette to get started. now works with ORCID’s v3 API (& new fxns); new fxns orcid_citations and orcid_search; many fixes
v0.3.0) of tacmagic is on CRAN - positron emission tomography time-activity curve analysis. See the release notes for changes. Checkout the vignette to get started. radioactivity unit conversion for tac objects and numeric objects; conversion of a tac object to standardized uptake value (SUV) by controlling for weight and injected dose
v0.4.0) of traits is on CRAN - species trait data from around the web. See the release notes for changes. Checkout the README to get started. many updates for betydb fxns; EOL Traitbank completely changed; bug fixes
v1.2) of hydroscoper is on CRAN - interface to the Greek National Data Bank for Hydrological and Meteorological Information http://www.hydroscope.gr/. See the release notes for changes. Checkout the vignettes to get started. removes plyr dependency
v1.3.1) of MtreeRing is on CRAN - a shiny application for automatic measurements of tree-ring widths on digital images. See the release notes for changes. Checkout the docs to get started. add plot parameter to
ring_read; all exported fxns renamed to snake_case style
v1.0.6) of skimr is on CRAN - compact and flexible summaries of data. See the release notes for changes. Checkout the vignettes to get started. v0.3.1) of cRegulome is on CRAN - access, manage and visualize regulome (microRNA/transcription factors)-gene correlations in cancer. See the release notes for changes. Checkout the vignettes to get started. fix a test
v2.0.0) of rdataretriever is on CRAN - R interface to the Data Retriever. See the release notes for changes. Checkout the README to get started. new author Hashit Bansal; add spatial support; now using reticulate; new
get_citationfxn
v1.0.1) of rcites is on CRAN - access the CITES Speciesplus database. See the release notes for changes. Checkout the docs to get started. now using cli pkg; bug fixes
v1.1.1) of bib2df is on CRAN - parse a BibTeX file to a data frame. See the release notes for changes. Checkout the vignette to get started. v0.1.1) of osmdata is on CRAN - import OpenStreetMap data as simple features or spatial objects. See the release notes for changes. Checkout the docs to get started. bug fix in
trim_osmdatafunction
v0.9.0) of biomartr is on CRAN - Genomic Data Retrieval. See the release notes for changes. Checkout the vignettes to get started. many new fxns and changes for existing fxns
v0.2.10) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. documentation fix
v1.4.0) of rtimicropem is on CRAN - supports the analysis of RTI MicroPEM output files. See the release notes for changes. Checkout the docs to get started. change dependency on pathological to fs
We accept community contributed packages via our onboarding system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system),and the authors of the packages!
If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following packages were recently submitted:
The following packages recently went through our onboarding process and have been approved:
We’re excited to announce the release of rOpenSci Dev Guide 0.2.0: Updates Inside and Out - authored by the rOpenSci Editors.
![](\"../assets/img/dev-guide-cover.png\")
Adam Sparks wrote a post POWER to the People about the nasapower package he maintains. The post includes how the package came about, some lessons learned during package development, and some cool usage examples.
![](\"../assets/img/nasapower-blog.png\")
Kshitiz Gupta and Carl Boettiger wrote a post on ramlegacy: a package for RAM Legacy Database for the ramlegacy package.
Matthias Grenié and Hugo Gruson wrote a post on Access Publisher Copyright & Self-Archiving Policies via the SHERPA/RoMEO API for their rromeo package.
Maëlle Salmon wrote a blog post about rodev: helpers for rOpenSci package authors. Check out the package.
Jeroen Ooms wrote about a significant piece infrastructure he’s been working on: Introducing the new rOpenSci docs server - a new service to automatically build and host documentation for all rOpenSci packages.
![](\"../assets/img/docs-server-jenkins.png\")
The following 17 works use/cite rOpenSci software:
There’s four recent use cases in the Use Cases section of the rOpenSci discussion forum:
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had six recent examples of maintainer transitions within rOpenSci:
We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.
Van den Berg, S. J. P., Baveco, H., Butler, E., De Laender, F., Focks, A., Franco, A., … Van den Brink, P. J. (2019). Modeling the Sensitivity of Aquatic Macroinvertebrates to Chemicals Using Traits. Environmental Science & Technology. https://doi.org/10.1021/acs.est.9b00893 ↩
Van Strien, M. J., Huber, S. H., Anderies, J. M., & Grêt-Regamey, A. (2019). Resilience in social-ecological systems: identifying stable and unstable equilibria with agent-based models. Ecology and Society, 24(2). https://doi.org/10.5751/es-10899-240208 ↩
Bayer, D., & Michael, S. (2019). Exploring the Daschle Collection using Text Mining. arXiv preprint arXiv:1904.12623 https://arxiv.org/pdf/1904.12623 ↩
Ruiz, J. L., & Gómez-Díaz, E. (2019). The second life of Plasmodium in the mosquito host: gene regulation on the move. Briefings in functional genomics. https://www.ncbi.nlm.nih.gov/pubmed/31058281 ↩
Baliga, V. B., & Mehta, R. S. (2019). Morphology, ecology, and biogeography of independent origins of cleaning behavior around the world. Integrative and comparative biology. https://doi.org/10.1093/icb/icz030 ↩
Estrela, M. J. (2019) JCSP 44 PCEMI 44 Master of Defence Studies Maîtrise en études de la défense. https://www.cfc.forces.gc.ca/papers/csc/csc44/mds/estrela.pdf ↩
Falster, D. S., FitzJohn, R. G., Pennell, M. W., & Cornwell, W. K. (2019). Datastorr: a workflow and package for delivering successive versions of “evolving data” directly into R. GigaScience, 8(5). https://doi.org/10.1093/gigascience/giz035 ↩
Barnett, A. G., & Moher, D. (2019). Turning the tables: A university league-table based on quality not quantity. F1000Research, 8, 583. https://doi.org/10.12688/f1000research.18453.1 ↩
Kovacevic, A., Latombe, G., & Chown, S. L. (2019). Rate dynamics of ectotherm responses to thermal stress. Proceedings of the Royal Society B: Biological Sciences, 286(1902), 20190174. https://doi.org/10.1098/rspb.2019.0174 ↩
Schindler, D., Yordanova, K., & Krüger, F. An annotation scheme for references to research artefacts in scientific publications. https://h-suwa.github.io/percomworkshops2019/papers/p52-schindler.pdf ↩
Piccione, P. M., Baumeister, J., Salvesen, T., Grosjean, C., Flores, Y., Groelly, E., … Lothschütz, C. (2019). Solvent Selection Methods and Tool. Organic Process Research & Development, 23(5), 998–1016. https://doi.org/10.1021/acs.oprd.9b00065 ↩
Łagód, G., Duda, S. M., Majerek, D., Szutt, A., & Dołhańczuk-Śródka, A. (2019). Application of Electronic Nose for Evaluation of Wastewater Treatment Process Effects at Full-Scale WWTP. Processes, 7(5), 251. https://doi.org/10.3390/pr7050251 ↩
Kirsch, S. A., & Böckmann, R. A. (2019). Coupling of Membrane Nanodomain Formation and Enhanced Electroporation near Phase Transition. Biophysical Journal. https://doi.org/10.1016/j.bpj.2019.04.024 ↩
Evans, K. M., Vidal-García, M., Tagliacollo, V. A., Taylor, S. J., & Fenolio, D. B. (2019). Bony Patchwork: Mosaic Patterns of Evolution in the Skull of Electric Fishes (Apteronotidae: Gymnotiformes). Integrative and Comparative Biology. https://doi.org/10.1093/icb/icz026 ↩
Jeremy Forbes, Dianne Cook, Rob J Hyndman. 2019. Spatial modelling of the two-party preferred vote in Australian federal elections: 2001-2016. Monash Econometrics and Business Statistics Working Papers 8/19, Monash University, Department of Econometrics and Business Statistics. https://ideas.repec.org/p/msh/ebswps/2019-8.html ↩
Colli‐Silva, M., Vasconcelos, T. N. C., & Pirani, J. R. (2019). Outstanding plant endemism levels strongly support the recognition of campo rupestre provinces in mountaintops of eastern South America. Journal of Biogeography. https://doi.org/10.1111/jbi.13585 ↩
Bhattarai, N., Mallick, K., Stuart, J., Vishwakarma, B. D., Niraula, R., Sen, S., & Jain, M. (2019). An automated multi-model evapotranspiration mapping framework using remotely sensed and reanalysis data. Remote Sensing of Environment, 229, 69–92. https://doi.org/10.1016/j.rse.2019.04.026 ↩